Where did the script come from? Wherever you found it I would avoid. There are a few problems with it that indicate that it is old or written by someone who doesn't know Perl very well.

For a start you should generally use chomp instead of chop.

([A-Z])([A-Z]) is better written ([A-Z]{2}).

The print should be a single line using string interpolation: print "$tree\n";

The substitution should use $1 instead of \1.

You should always use strictures (use strict; use warnings;).

Update: too enthusiastic finding improvements

Did you want the final line of output to be this:

(ABE)
[download]

(A(((BC)D)(EF)))
(A(((BC)D)(EF)))
(A((BD)(EF)))
(A((BD)(EF)))
(A(B(EF)))
(A(B(EF)))
(A(BE))
(A(BE))
(AB)
(AB)
A
[download]

Could be the progression you require, otherwise as stated above you end up with (ABE).

If that is what you require, then this could be what you need, if not, it's a starting point ;)

s/\(([^)])[^)]\)/$1/
[download]

If so, you'll need to insert some []s to indicate that A-Z is one of a range of characters

I personally believe that (s)he has inserted those []'s, except that not having put code inside <code> tags as (s)he should have they rendered like hyperlinks due to the shortcuts available as part of the markup here at the monastery, à la A-Z. (ATM, that is: at a later time, someone reading this thread may hopefully find the root node duly edited...) To see the code closer to the way the OP really meant it you could try the xml view of the node.

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