You need to be more selective about what you are matching, and will have to repeat the substitution until all nested matches are removed 
use strict;
use warnings;
my $string="TestVar(Test1->(xy))->Var2(Test2(10)(12))->Finalvar"; 
while ($string=~s/   # repeat while we make matches
\(                   #beginning of a parenthesised group
[^)(]+               # non parentheses charaters 
\)                   # end of group
//gx)
{}
print "$string\n";

[download]
This will remove parenthesised groups, starting from the innermost

Edit: tidied up comments in code block

print "Good ",qw(night morning afternoon evening)[(localtime)[2]/6]," fellow monks."

In reply to Re: Regex required to Replace the array specifiers in a string by Utilitarian
in thread Regex required to Replace the array specifiers in a string by anandvn

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