My guess is that you have tailored your program to work with the logic in this subroutine (or that it's an accidental success).

perldoc -f do says:

"do BLOCK" does not count as a loop, so the loop control statements "next", "last", or "redo" cannot be used to leave or restart the block. See perlsyn for alternative strategies.

More details are available in perlsyn

One way what you've written would work could be described as:

1) you repeatedly call my $line = nextline( $fh );
2) the first line of the do block reads a line off of your filehandle.
3 a) if that line is a comment, the subroutine exits via next (next doesn't go to the next iteration of the do block (as we learned from the documentation)).
3 b) if that line isn't a comment, it's assigned to $l (via clean()).
4) this happens until $l ne ''.

Since even "blank" lines will contain a newline, the until conditional will guarantee that your do block is only entered once (even for non-comment lines).

Hope that helps a little,

-- Douglas