Is there another way?

Remove comments from the input before matching.

For trivial code containing only // comments (not /* */) and without string constants containing //, the following should do the trick:

#!/usr/bin/perl
use strict;
use warnings;
while (<>) {
    chomp;
    my $orig=$_;
    s|//.*||; # strip comments
    if (/\b(printf|scanf|open|close|read|write)\b/) {
        print "Found keyword '$1' in '$_'.\nOriginal line: '$orig'\n";
    }
}
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Alexander