Copy and Paste would not be much good if it didn't actually do what it says, so YES it works.
Now when you say "perfect copy" ... Whether you know it or not hard drives are formatted into sectors. Files can use from 1 or more sectors, with each sector linked to the next and an EOF (end of file) marker in the last. Any information beyond the EOF is considered random and useless so whether or not that gets copied or not is not consistent (sometimes hackers try to hide code here so if that is your question then go elsewhere). Also sectors on one harddrive may not be the same size as the destination so some restructuring will occur automatically when you copy, so you won't have identical sectors but you will have identical useable data; it will all be there and function exactly the same.
Yes there are tools to compare, see
HERE. Try
WinMerge.