If I understand correctly your question, yes, you can use the same filehandler successively for processing different files, provided that you open each file, process it and close it successively. This is an example Perl one-liner where I use the same $IN handler to process (in this case just print to the screen) successively two files:

$ perl -e 'for my $file (qw /pattern.pl line_count.pl /) {open my $IN,
+ "<", $file or die $!; print while <$IN>; close $IN;}'
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This prints to my screen the content of the "pattern.pl" and "line_count.pl" files. (There are easier ways to do just that, e.g. using the "p" command line option, but the aim here is just to demonstrate the syntax. An additional remark is that it is not even necessary to close the files in the example above, because the files would be closed automatically when the lexical filehandler goes out of scope at the end of the loop iteration, but I consider it is better to do it explicitly.)