Did you try implementing the readObject and writeObject methods?
http://java.sun.com/j2se/1.5.0/docs/api/java/io/Serializable.html

   - Oliver

How deep? Must be thousands or millions.

Your options are:

1) Change your data structure (I know you said you don't want to do that, but
you may have to anyway).

2) Implement a custorm representation within the serialisation framwork (as
Oliver has already suggested).  Note that the essential problem is with your
datastructure, so you will still have to find a solution to the underlyng
problem -- perhaps by using an explicit stack rather than the Java thread's
stack.

3) Find/Implement a complete replacement for serialisation.  Same caveat
applies as in (2), which makes it unlikely that an existing solution will work
for you without change.

4) Translate the structure into another form and serialise that.  Similarly
rebuild your intended structure from the serialised from as you read it in.
This is roughly equivalent to (2) but may be easier to implement depending on
what you are doing.

5) Quit and find another job.

I.e. there are no easy answers -- you are going to have to do quite a lot of
work no matter how you approach it.

   -- chris

Note that this does NOT work for the initial thread. You may want to
let the serialization code run in a thread with a larger stack (which
you can specify on thread creation time, if I remember correctly.)

You may want to serialize a somewhat flattened data structure. For
example, a tree could be flattened to a list.