I do this all the time, works fine, just be sure to use binmode after you open the file, then slurp the whole file into a string (reading line-by-line makes no sense with a binary file). For example:

use strict;
open(my $fh, '<', 'some_binary_file') or die;
binmode($fh);
my $file_contents = do { local $/; <$fh> };
close($fh);
$file_contents =~ /some-string/ and print "it matched\n";
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