When you are uploading a file via an HTML form you can access this file using CGI.pm.
If you are creating the HTML with CGI as well, the upload field can be created like this:

print $query->filefield(-name=>'uploaded_file',
                        -default=>'starting value',
                        -size=>50,
                        -maxlength=>80);
[download]

Usually these files are uploaded into a temoporary directory. CGI.pm deletes them automatically from the tmp dir after processing.
Access the file like this:

$filename = $query->param('uploaded_file');
$type = $query->uploadInfo($filename)->{'Content-Type'};
# or
$fh = $query->upload('uploaded_file');
while (<$fh>) {
     print;
}
[download]