Doing nested parenthesis (or any paired delimiter) in regular expressions is not trivial. In your case, it is a little simpler since you are trying to strip out all parentheticals. You can accomplish your task by repeatedly running a substitution that eliminates inner-most pairs, like:

$_ = "TestVar(Test1->(xy))->Var2(Test2(10)(12))->Finalvar";
1 while (s/\([^()]*\)//g);
print;
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I repeatedly substitute matched sets of parentheses to blank strings, where I ensure the parentheses do not contain other parentheses Using character classes. See perlretut for more info.