|Do you know where your variables are?|
$line =~ s/(.*)\,(.*)\,(.*)\,(.*)\,(.*)\,(.*)/
Why are you escaping all those commas? A comma has no special regex meaning. In a regex, a comma means one thing: a literal comma.
The pattern .* says to match ANY character, 0 or more times, GREEDILY. That means that the regex engine will match as many characters as possible. When the regex engine sees a pattern like:
...the first thing the regex engine does is find a match for the part in parentheses. Your whole line matches that part, so the regex engine reads in your whole line as the match for (.*). Then the regex engine moves on to the comma. Because there are no characters remaining in the line to match against, the regex engine backs up one character, surrendering a character from what matched .*. Then the regex engine checks if the comma matches that character. No match. So the regex engine backs up another character, surrendering yet another character from what matched .*, and the regex engine checks again if that character matches the comma. So on and so on until the regex finds a match for the comma. That's inefficient.
A more efficient regex would be this:([^,]+),([^,]+)
However, as tmharish already mentioned you already split() your data, so there is no reason to use a regex at all. Just change whatever pieces you want in @fields like this:
You can limit your split to 5 instead of on every comma, which will speed things up a little.
It is possible to do a conditional s///, like this:
(The /e flag stands for eval.) But that is much slower than split() + join().
There is no reason to use Text::CSV_XS or any other CSV module.