Have you considered using Parse::RecDescent? It implements a full-featured recursive-descent parser. A real parser (as opposed to parsing a string with a regular expression alone) is much more powerful and can be more apropriate for parsing highly structured/nested data like you have. I'm not sure exactly what you want to do with the line after you parse it, so my example below does't do anything with the data it parses, but it should be a good starting point if you want to try using Parse::RecDescent to parse your data. (it has been a while since I've written a grammer so it may look a bit rough).

use Parse::RecDescent;
my $teststr="blah1,blah2(blah3,blah4(blah5,blah6(blah7))),blah8";
my $grammar = q {
        content:        /[^\)\(\,]+/
        function:       content '(' list ')'
        value:          content
        item:           function | value
        list:           item ',' list | item
        startrule:      list
};
my $parser = new Parse::RecDescent ($grammar) or die "Bad grammar!\n";
defined $parser->startrule($teststr) or print "Bad text!\n";
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