Simply stated, '.' refers to the current directory; '..' refers to the current directory's parent. Trying to copy those causes problems, and is usually not what you intend. However, readdir reads those two as 'files', so you have to skip them.

If you're still getting errors, you may need to check that you're actually creating the directories you think you are. In particular, I am suspcious of the ending backslash, which I believe may be an error. So - omitting the copy, are your directories actually being created? Also, I'm thinking that you need to be using forward slashes, even though you're on Windows. I know I do well enough when I use $dir="level1/level2/etc"; (note the double quotes). You can use this form for specifying a file path:  $path="$dir/$file";, which works.