Rather than a global match you could use a while statement modifier.

knoppix@Microknoppix:~$ perl -E '
> $file = <<EOD;
> some data; comment 1
> more data; comment 2
> even more data; comment 3
> EOD
> push @comments, $1 while $file =~ s{(;[^\n]*)}{*MARKER*};
> say $file;
> say for @comments;'
some data*MARKER*
more data*MARKER*
even more data*MARKER*

; comment 1
; comment 2
; comment 3
knoppix@Microknoppix:~$
[download]

I hope this is of interest.