Ok, sorry. The command line output given by the exception is this:

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
       at Application.closeFile(GMLV.java:179)
       at Application.actionPerformed(GMLV.java:103)
       at javax.swing.AbstractButton.fireActionPerformed(Unknown
Source)
       at javax.swing.AbstractButton$Handler.actionPerformed(Unknown
Source)
       at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown
Source)
       at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
       at
javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Sour
ce)
       at java.awt.Component.processMouseEvent(Unknown Source)
       at javax.swing.JComponent.processMouseEvent(Unknown Source)
       at java.awt.Component.processEvent(Unknown Source)
       at java.awt.Container.processEvent(Unknown Source)
       at java.awt.Component.dispatchEventImpl(Unknown Source)
       at java.awt.Container.dispatchEventImpl(Unknown Source)
       at java.awt.Component.dispatchEvent(Unknown Source)
       at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown
Source)
       at java.awt.LightweightDispatcher.processMouseEvent(Unknown
Source)
       at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
       at java.awt.Container.dispatchEventImpl(Unknown Source)
       at java.awt.Window.dispatchEventImpl(Unknown Source)
       at java.awt.Component.dispatchEvent(Unknown Source)
       at java.awt.EventQueue.dispatchEvent(Unknown Source)
       at
java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)

       at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown
Source)
       at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
       at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
       at java.awt.EventDispatchThread.run(Unknown Source)

So the exception is related to the 'Close' button to close a file.
Here is the full code, it might not be the most efficient or elegant
code, but it is my first attempt at a Java application so I'm not too
worried about that as long as it works! ;-)

import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
import java.io.*;

public class GMLV
{
    public static void main(String args[])
    {
        Application application = new Application();
    }
}

class Application extends JFrame implements ActionListener
{
    // create components to make them globally available to event handlers
    // create toolbar buttons
    JButton toolbarLoad = new JButton("Load");
    JButton toolbarClose = new JButton("Close");
    JButton toolbarHelp = new JButton("Help");

    // create menu and items
    JMenuItem menuLoad = new JMenuItem("Load");
    JMenuItem menuClose = new JMenuItem("Close");
    JMenuItem menuExit = new JMenuItem("Exit");
    JMenuItem menuAbout = new JMenuItem("About");
    JMenuItem menuOverview = new JMenuItem("Overview");
    JMenuBar menubar = new JMenuBar();
    JMenu fileMenu = new JMenu("File");
    JMenu helpMenu = new JMenu("Help");
    public JTextArea blank = new JTextArea(30, 70);

    // create input
    public FileReader fileReader;
    public BufferedReader buffer;

    // constructor
    public Application()
    {
        super("GeotechML Visualizer");
        int windowWidth = 800;
        int windowHeight = 650;

        // set window to centre of screen
        Point center =
GraphicsEnvironment.getLocalGraphicsEnvironment().getCenterPoint();
        setBounds(center.x-windowWidth/2, center.y-windowHeight/2,
windowWidth, windowHeight);
        setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
        setVisible(true);

        // add toolbar button event listeners
        toolbarLoad.addActionListener(this);
        toolbarClose.addActionListener(this);
        toolbarHelp.addActionListener(this);

        // add toolbar buttons to toolbar
        JToolBar toolbar = new JToolBar();
        toolbar.add(toolbarLoad);
        toolbar.add(toolbarClose);
        toolbar.add(toolbarHelp);

        // add menu item event listeners
        menuLoad.addActionListener(this);
        menuClose.addActionListener(this);
        menuExit.addActionListener(this);
        menuOverview.addActionListener(this);
        menuAbout.addActionListener(this);

        // add items to menu
        fileMenu.add(menuLoad);
        fileMenu.add(menuClose);
        fileMenu.addSeparator();
        fileMenu.add(menuExit);
        helpMenu.add(menuOverview);
        helpMenu.add(menuAbout);
        menubar.add(fileMenu);
        menubar.add(helpMenu);

        // add components to container
        menuLoad.setEnabled(true);
        menuClose.setEnabled(false);
        toolbarLoad.setEnabled(true);
        toolbarClose.setEnabled(false);
        blank.setEditable(false);
        JScrollPane scroll = new JScrollPane(blank);
        BorderLayout mainLayout = new BorderLayout();
        setLayout(mainLayout);
        setJMenuBar(menubar);
        add(scroll, "Center");
        add(toolbar, "North");
        pack();
    }

    public void actionPerformed(ActionEvent event)
    {
        Object source = event.getSource();

        // toolbar button events
        if (source==toolbarLoad) {
            this.loadFileChooser();
        }
        if (source==toolbarClose) {
            this.closeFile();
        }
        if (source==toolbarHelp) {
            HelpWindow help = new HelpWindow();
        }

        // menu item events
        if (source==menuClose) {
            this.closeFile();
        }
        if (source==menuLoad) {
            this.loadFileChooser();
        }
        if (source==menuExit) {
            System.exit(0);
        }
        if (source==menuOverview) {
            HelpWindow help = new HelpWindow();
        }
        if (source==menuAbout) {
            AboutWindow about = new AboutWindow();
        }
    }

    public void loadFileChooser()
    {
        JFileChooser chooser = new JFileChooser();
        chooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
        int result = chooser.showOpenDialog(this);
        if (result == JFileChooser.CANCEL_OPTION) return;
        File filename = chooser.getSelectedFile();
        if (filename == null || filename.getName().equals("") )
        {
            JOptionPane.showMessageDialog(this,"Invalid File Name","Invalid File
Name",JOptionPane.ERROR_MESSAGE);
        }
        else
        {
            try
            {
                BufferedReader buffer = new BufferedReader(new
FileReader(filename));

                // enable close button and disable load button (currently, only one
buffer may be open at once)
                menuLoad.setEnabled(false);
                menuClose.setEnabled(true);
                toolbarLoad.setEnabled(false);
                toolbarClose.setEnabled(true);

                // test
                boolean eof = false;
                while (!eof)
                {
                    String lineInput = buffer.readLine();
                    String printLine = "\n" + lineInput;
                    if (lineInput == null)
                    {
                        eof = true;
                    }
                    else
                    {
                        blank.append(printLine);
                    }
                }
            }
            catch (IOException openError)
            {
                JOptionPane.showMessageDialog(this, "Error Opening File", "Error",
JOptionPane.ERROR_MESSAGE);
            }
        }
    }

    public void closeFile()
    {
        try
        {
            blank.setText("");
            buffer.close();
            menuLoad.setEnabled(true);
            menuClose.setEnabled(false);
            toolbarLoad.setEnabled(true);
            toolbarClose.setEnabled(false);
        }
        catch (IOException closeError)
        {
            JOptionPane.showMessageDialog(this, "Error Closing File", "Error",
JOptionPane.ERROR_MESSAGE);
        }
    }
}

class AboutWindow extends JFrame implements ActionListener
{
    JButton closeButton = new JButton("Close");

    public AboutWindow()
    {
        super("About GeotechML Visualizer");
        int aboutWindowWidth = 400;
        int aboutWindowHeight = 250;
        String about = "\n\nA Java visualizer for GeotechML data
files\nDeveloped as part of Stephen Marjoribanks' MEng final year
project\nVersion 0.1b\n\nCopyright 2006, S Marjoribanks, University of
Durham\n\n";

        // set window to centre of screen
        Point center =
GraphicsEnvironment.getLocalGraphicsEnvironment().getCenterPoint();
        setBounds(center.x-aboutWindowWidth/2, center.y-aboutWindowHeight/2,
aboutWindowWidth, aboutWindowHeight);
        setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
        setVisible(true);

        // create layout
        BorderLayout aboutLayout = new BorderLayout();
        setLayout(aboutLayout);

        // create and add components
        setResizable(false);
        JPanel aboutPanel = new JPanel();
        JTextArea aboutText = new JTextArea(about);
        aboutText.setEditable(false);
        closeButton.addActionListener(this);
        aboutPanel.add(aboutText, BorderLayout.CENTER);
        add(closeButton, BorderLayout.SOUTH);
        add(aboutPanel);
        pack();
    }

    public void actionPerformed(ActionEvent event)
    {
        Object source = event.getSource();
        if (source==closeButton) {
            dispose();
        }
    }
}

// HelpWindow class will be modified later to contain help information
class HelpWindow extends JFrame
{
    public HelpWindow()
    {
        super("GeotechML Visualizer Help");
        int helpWindowWidth = 400;
        int helpWindowHeight = 500;
        String help = "Enter help information here\n";

        // set window to centre of screen
        Point center =
GraphicsEnvironment.getLocalGraphicsEnvironment().getCenterPoint();
        setBounds(center.x-helpWindowWidth/2, center.y-helpWindowHeight/2,
helpWindowWidth, helpWindowHeight);
        setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
        setVisible(true);

        // create container
        JPanel helpPanel = new JPanel();
        BorderLayout helpLayout = new BorderLayout();
        helpPanel.setLayout(helpLayout);
        JTextArea textArea = new JTextArea(help);
        textArea.setEditable(false);
        JScrollPane scroll = new JScrollPane(textArea,
ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED,
                                                  ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
        helpPanel.add(scroll);
        add(helpPanel);
        pack();
    }
}

Thanks for your help!

Steve