Do not name flags $flag. If you give flags such meaningless names, then one of the more common errors in your code will be that you accidentally reverse the meaning of a flag.

Instead give flags names which are yes/no questions, which the flag's value is an answer to. Now you'll never have trouble keeping it straight, and nor will anyone else who glances at your code.

If you think this advice is silly, then remind yourself of it the next time you catch a bug due to your accidentally reversing a flag's meaning...

To echo what tilly said, don't use 'flag' for a variable name unless you're talking about a square or rectangle of cloth. Why not something more interesting like $seenJunkYet instead?

I'd rather go for something like

#  Skip header junk
while(<>) {
  last if /end of header junk/;
}
#  Start processing real data
while(<>) {
  #  But quit if we see junk starting up again
  last if /start of trailer junk/;

  # Do useful stuff here
}
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This is fairly common task

Indeed, yesterday someone asked for this.