foreach (@files) {
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foreach my $file (@files) {
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    $outputfile = "STEP2_" . $_;
    open(OUTFILE, ">" , $outputfile) or die $!;
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    $outputfile = "STEP2_" . $file;
    open(OUTFILE, ">" , $outputfile) or die "opening $outputfile $!";
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Revise: The foreach was corrected, thanks to moritz kindly pointing out my gaffe.

With Perl 5.8.5, I can't reproduce your error. I've changed your code around a bit to make it work with strict and removed some of the file tests because they are redundant but still:

use strict;

my @files = qw(CaseComment.csv);
my $dir1 = ".";
my $dir2 = ".";

########################
# OPEN THE STEP 1 FILE #
########################
foreach (@files) {
    my $filename = "$dir1/$_";
    #chdir($dir1); # replace by "$dir/$_"
    
    # Redundant - open() will die with
    # an informative message anyway
    ## Verify Files exist
    #die "File: '$filename' does not exist: $!"
    #   unless -e $filename;
    ## Verify Files are read/writable
    #die "File: $filename isn't read or writable \n $!"
    #    unless ((-r $filename ) && (-w $filename ));
    
    ### Open the file
    open (FILE, "<", $filename ) or die "Cannot open the file '$filena
+me': $!\n";
    #select((select(FILE), $/ = undef)[0]); # what is that for?
    
    my @array_contents = <FILE>;
    
    close (FILE) or die $!;

## DO SOME STUFF
##########################
# CREATE THE STEP 2 FILE #
##########################
    #chdir($dir2);
    
    my $contents = <<TESTCOMMENTS;
Line 1
line 2
linE 3
TESTCOMMENTS
    
    my $outputfile = "$dir2/STEP2_" . $_;
    warn "Writing '$contents'";
    open(OUTFILE, ">" , $outputfile) or die "Couldn't create '$outputf
+ile':$!";
    print OUTFILE $contents;
    close OUTFILE or die $!;
};


##########################
# ACCESS THE STEP 2 FILE #
##########################

#chdir($dir2);
my $commentsfile = "$dir2/STEP2_CaseComment.csv";
open (SFCOMMENTS, "<", $commentsfile) or die "Cannot open Salesforce C
+omments file '$commentsfile' : $! \n";
my $count = 0;
while (<SFCOMMENTS>) {
    print "Count is: $count \n";
    $count ++;
}
close SFCOMMENTS or die $!;
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C:\Projekte>perl -w tmp.pl
Writing 'Line 1
line 2
linE 3
' at tmp.pl line 44.
Count is: 0
Count is: 1
Count is: 2
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Maybe your assignment to $contents is somehow wrong? More debugging information is needed.

I don't see where your problem has anything to do with the ordering of opens and closes. More likely the records are not getting written correctly. Your code slurps the contents of the input file as one record into the first element of @array_contents then writes $contents out to the second file without any record delimiters. The code provided does nothing when I run it. Have you verified the contents of your written file using a text editor? Can you provide a snippet of code that behaves as you say?

Two other minor points. You call chdir() inside your foreach(@files) loop. This will only work for absolute path names otherwise the code will try to chdir to a subdirectory from inside a subdirectory. The $count loop displays the first record as a count of 0. While it would be proper to consider this an index of 0, the count should read 1.