The best solution is probably to do a match followed by a substitution, as suggested by jettero, BrowserUk and explorer but it can be done with a regular expression, or two in fact. The first uses regular expression recursion to successively match groups of digits followed by a comma or closing parenthesis, appending the captured digits to a variable using a code block. The second initialises the variable then incorporates the first.

use strict;
use warnings;

use re q{eval};

my @numbers = (
   q{Number... ()},
   q{Number... (1)},
   q{Number... (12)},
   q{Number... (123)},
   q{Number... (1,234)},
   q{Number... (12,345)},
   q{Number... (123,456)},
   q{Number... (1,234,567)},
   q{Number... (12,345,678)},
   q{Number... (123,456,789)},
   q{Number... (1,234,567,890)},
   q{Number... (1,234a)},);

my $deCommafied;

my $rxNumberGrps;
$rxNumberGrps = qr
   {(?x)
       \D*
       (\d+)
       (?=,|\))
       (?{$deCommafied .= $^N})
       (?:
          (??{$rxNumberGrps})
          |
          \)\z
       )
   };
my $rxDeComma = qr
   {(?x)
       (?{$deCommafied = q{}})
       $rxNumberGrps
   };

foreach my $number (@numbers)
{
    print
       qq{$number - },
       $number =~ m{$rxDeComma}
       ? qq{$deCommafied\n}
       : qq{no match\n};
}
[download]

Here's the output.

Number... () - no match
Number... (1) - 1
Number... (12) - 12
Number... (123) - 123
Number... (1,234) - 1234
Number... (12,345) - 12345
Number... (123,456) - 123456
Number... (1,234,567) - 1234567
Number... (12,345,678) - 12345678
Number... (123,456,789) - 123456789
Number... (1,234,567,890) - 1234567890
Number... (1,234a) - no match
[download]

As I said, the match and substitute approach is much simpler and easier to understand. This solution is far too complicated to maintain and was done more for the challenge as I'm not very good at recursion.

Cheers,

JohnGG