As with most regular expressions, the following is assuming a whole lot. For example that there are not more embedded functions in the functions that occur inside the first function. Also that there are only 4 arguments (parameters?) passed to the first function. Lastly that there are no spaces between the argument and the comma. You might have to modify this to get the spacing (adding \s in places and whatnot. Anyhow here is some code that might work for your purpose:

use strict;
use warnings;

while ( <DATA> ) {
  my $string = $_;
  if ( $string =~ /func[A-Za-z]\(
        (func[A-Za-z]\([^\)]+\)|[^,]+)         #looks for a function a
+nd if not found then
       ,(func[A-Za-z]\([^\)]+\)|[^,]+)        #grab everything to the 
+comma
       ,(func[A-Za-z]\([^\)]+\)|[^,]+)
      ,(func[A-Za-z]\([^\)]+\)|[^,]+)\)/x)
  {
    print "FOR STRING: $string",
          '$1 = ',$1,$/,
          '$2 = ',$2,$/,
          '$3 = ',$3,$/,
          '$4 = ',$4,$/,$/;
  }
}


__DATA__
funca(1,2,3,4)
funca(funcH(A,B,C),2,3,4)
funca(1,funcH(A,B,C),3,4)
funca(1,2,funcH(A,B,C),4)
funca(1,2,3,funcH(A,B,C))
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Updated:Removed some of the ugliness from the formatting in code.

-enlil