use Getopt::Long   qw( GetOptions );
use File::Basename qw( basename );

sub usage {
   my ($msg) = @_;
   print STDERR $msg if defined($msg);
   my $fn = basename($0);
   print STDERR "usage: $fn ...\n";    # XXX Fill in the "..."
   exit(1);
}

GetOptions(
   'a=s' => my $alignment_file,
   's=s' => my $scorecons_file,
   'i=s' => my $image_file,
   'm=s' => my $numbered_model,
   'c=s' => my $csa_file,
) or usage();

defined($alignment_file) or usage("Missing alignment file\n");
defined($scorecons_file) or usage("Missing score file\n");
defined($image_file    ) or usage("Missing image file\n");
defined($numbered_model) or usage("Missing numbered model file\n");
defined($csa_file      ) or usage("Missing CSA file\n");
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Assuming that the cause of your error in present within your code snippet, the warning is being thrown by your print statement. Specifically, variable interpolation within double quotes is implicitly done with the concatenation operator, thus when you attempt to print without first initializing $csa_file, warnings notes you are concatenating with an undefined value. See String interpolation. I suspect this error is the result from your misplaced curly bracket. Perhaps you mean something like this:

#_ Command line options & setup filenames
for ($i=0; $i<=$#ARGV; $i++)
{
    if($ARGV[$i] eq "-a")
    {
    $alignment_file = $ARGV[$i+1];
    }
    if($ARGV[$i] eq "-s")
    {
    $scorecons_file = $ARGV[$i+1];
    }
    if($ARGV[$i] eq "-i")
    {
    $image_file = $ARGV[$i+1];
    }
    if($ARGV[$i] eq "-m")
    {
    $numbered_model = $ARGV[$i+1];
    }
    if($ARGV[$i] eq "-c")
    {
    $csa_file = $ARGV[$i+1];    
    }
}
print "test $csa_file\n";
    
#_ Check for minimum number of command line argument variables
if($#ARGV < 6)
{
    Usage();
    print "NOT ENOUGH COMMAND LINE ARGUMENTS\n";
    exit 0;
}
    
$fh_csa = new FileHandle($csa_file, "r") || die "Cannot open CSA file:
+ $csa_file ($!)";
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Some side notes on style:

1. Generally, the lower precedence or is used in testing in place of the high precedence || you have used to test your file open. It doesn't matter here, but it will matter in similar constructs, such as if you omit parentheses on an argument list.
2. Foreach constructs tend to be more resilient than C-style for loops. Consider that replacing your for loop with:

   foreach my $i (0 .. $#ARGV)

3. You are obviously using warnings given then message you report, but are not using strictures. You can avoid a lot of headaches if you use strict.

Update: Your update supports the conclusion that you have a brackets probelm. You are only evaluating the first term of your argument list opening your file and continuing.

Well actually I am using strict. But thanks for the help :)I will see if that helps

My update was poorly worded (fixed). The supported conclusion is that your blocks are not structured like you expect. Try it with the posted code.

I find it surprising that you are using strict, given that there are no my statements in your snippet. It is a bad idea to use loop variables that are not limited to that loop in scope. This is particularly risky with C-style loops.

yep, that sorted it. Thanks