(Update: mis-read your question, but still applies. Some text below updated to match your request.)

If your task is simple or straightforward, you may just get away with the magic <> line iterator. This automatically pulls from each named file in turn, or from STDIN if there was none. This handles both of your cases magically.

# receive a list of filenames on stdin
# (or from an intermediary file named on command line)
#
while (<>)
{
   chomp;
   # process a filename in $_
}
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If you're new to Perl, I would also try to ween you away from "index loops" and toward iterating over the elements. You will find that you rarely NEED the integer representing the current position in a group of things.

# index loop
for my $f (0 .. $#array)
{ my $g = $array[$f];
  ...
}

# element loop
for my $g (@array)
{ ...
}
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