how can I generate a unique filehandle for each output file to then later use with print statements?

Store all the filehandles as values in a single hash which is keyed on the unique names (whether you use the actual filenames as keys or something symbolic is up to you). This way you can (a) pick a filehandle by key at any time and (b) iterate over all of them should the need arise.

In reply to Re: Opening multiple output files within a loop by hippo
in thread Opening multiple output files within a loop by TJCooper

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