Memory issues are usually difficult to track. How do you seriously expect us to help you on such issues if you don't post the real program but only pseudo-code, or don't post, at the very least, a modified/simplified program that exhibits the same behavior as the one you are describing? The code you presented is poorly written in terms of memory management and variable scoping and a number of other aspects (I would simply not hire someone who shows to me such code with no indentation whatsoever), but I don't believe for one second that this code would continue to clutter memory after the program has completed.

Do yourself a favor: remove all these silly undef function calls and use correctly scoped lexical variables, use strict;, use warnings;, indent your code correctly (with whatever indenting style you prefer), give variables meaningful names, learn how to use arrays and hashes, rather than things like

$var1=$1;$var2=$2;$var3=$3;$var4=$4;
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Your code will be twice shorter and far more readable.