Well, it's late here, but this will get you started:

#!/usr/bin/perl -w
use strict;
open (FILE1, "input.txt");
open (FILE2, ">output.txt");
while (<FILE1>)
{
        /^(.+?)\s{1,9}(.+?)\s{1,9}(.+?)$/;
        print FILE2 "$1,$2,$3\n";
}
close FILE2;
close FILE1;
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Open two files, one for input and the other for output. Read each line in the first, matching the fields. On my example, I match (barely, that regexp is totally half-baked) 3 fields, with 1 up to 9 spaces between them. Store the matched fields in the regexp's history variables ($1/$2/$3), then output that to the file.

Is this what you wanted?