First, when uploading multiple files with a single POST, you must have a separate file param for each file:

<input type="file" name="file1">
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Second, you get the remote filename with param. Then change this into the local filename.

my $filename = $cgi->param('file1');
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Third, you get the filehande with upload:

my $fh = $cgi->upload('file1');
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Fourth, get the uploaded Content-Type (has absolutely ntohing to do with the page's Content-Type) with uploadInfo

my $content_type = $cgi->uploadInfo($filename)->{'Content-Type'};
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I would suggest writing a function that handles a single file upload. And then call it multiple times for each file param in the form.

upload_file('file1');
upload_fiel('file2');

sub upload_file {
   my ($param_name) = @_;
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