Why do you think HTML::FillInForm works with HTML::Tree instances internaly??? If it did, it would be trivial to change it to allow you to pass one instead of passing a string from which a tree is built. But the module doesn't build any tree. It processes the HTML using HTML::Parser and callbacks. No tree involved. At least in the 2.00 version on CPAN.

If you'd want to skip the conversion from tree to string and back, you'd have to reimplement the module. So that the start(), text() and end() methods are called as you traverse the list and inside those methods instead of appending to $self->{output} you'd have to build the result tree or modify the original one. I think you could use a lot of the code with fairly small changes.