The basic answer is you cannot extract a single entity from two discontiguous parts of a string using a regex alone. If you extracted the bits using regex captures, you'd have to concatentate them together at some point. And as there is no way to write a repeated capture, it's gonna get messy trying when there are a variable number of parts to capture.

Your simplest method, as you mentioned, would be to extract the contents of the parens and then remove the commas.

print "$_ : ",  do{ 
    ($_) = m[ \( ( [^)]+ ) \) ]x; 
    tr[,][]d; 
    $_ 
} for map "($_)", qw[ 1,234 1,234,567 1,234,567,890 ];;

(1,234) :  1234
(1,234,567) :  1234567
(1,234,567,890) :  1234567890
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