one thing to consider in the below code is that a "directory" is a file. This means the "." and ".." are files too! I congratulate you on using readdir rather than "globbing". This is much more portable and is the right way to go. I would put a grep to filter to the "real files",

opendir(DIR, $RemoteSubDirectory);
my @rFileCheck = grep {-f $RemoteSubDirectory/$_ }readdir(DIR);
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Remember that readdir only gives file names and you have to add the path... Your code:

opendir(DIR, $RemoteSubDirectory);
my @rFileCheck = readdir(DIR);
closedir(DIR);
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