Slashes and $ have special meaning in regexps, so you need to escape them. You've escaped them for the quotes (to tell the quotes they are not special), but you didn't also escape them for the regexp to tell the regexp they are not special. You want

my $ndata = "\\\\MYSERVER\\C\$\\Temp";  # \\MYSERVER\C$\Temp
my $quoted_ndata = quotemeta($ndata);   # \\\\MYSERVER\\C\$\\Temp
m/$quoted_ndata/
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or

my $ndata = "\\\\MYSERVER\\C\$\\Temp";  # \\MYSERVER\C$\Temp
m/\Q$ndata\E/
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You want to locate $ndata at the begining of $line, so you need to add ^, as follows:

m/^\Q$ndata\E/
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Don't use $'. It will slow down every regexp in your program that doesn't have captures. Use the following instead:

if ($line =~ m/^\Q$ndata\E(.*)/) {
   my $ndir = $1;
   print "$ndir\n";
}
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Finally, searching for a constant string using a regexp is inefficient. Use the following instead:

if (index($line, $ndata) == 0) {
   my $ndir = substr($line, length($ndata));
   print "$ndir\n";
}
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Updated.