One option is to use one of the wonderful templateing modules, like HTML::Template. I switched to that after years of rolling out my own templates, and I've never looked back.

However, if you can't use a module, or perhaps don't want to, you could do something like this:

# It's good practice to make sure your open succeeds
open(FILE,$template) or die "Can't read template: $!";

# while instead of foreach, since while (since it's 
# scalar context) reads the FILE a line at a time, instead 
# of slurping it all into memory
while (<FILE>) {
  # replace only your match with the return value of the sub
  s/MY_MATCH/&do_something/eg;
  print;
}
close FILE;
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-- Dan