@folders=glob("*"); #to get all folders in directory; extension ("*") 
+as wildcard to get all names
foreach$folder(@folders) #to speak to each element in directory
    {
    next if ($folder!~/^UNITAS_/); #skip elements which do not start w
+ith "UNITAS"
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Because you are only interested in "folders" that begin with the string "UNITAS_" you can do that with glob:

# to get UNITAS_* folders in directory
my @folders = glob "UNITAS_*";
# to speak to each element in directory
foreach my $folder ( @folders )
    {
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        $head=<TRF>; #remove the first four lines of the trf-table.txt
+ file
        $head=<TRF>;
        $head=<TRF>;
        $head=<TRF>;
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You don't need a variable to do that:

        undef = <TRF>; #remove the first four lines of the trf-table.t
+xt file
        undef = <TRF>;
        undef = <TRF>;
        undef = <TRF>;
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Or use a loop:

        # remove the first four lines of the trf-table.txt file
        undef = <TRF> for 1 .. 4;
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