Thanks for the reply,
But unfortunately it doesn't because:
1) Even if i manage to move all files to correct location i still have couple hundred of empty folders.
2) This is how it works in my environment:
I've have a mapped drive on my user that's running this script (my server), with this command I'm providing a source something like "Y:\SourceFiles\Folder1\File1.dll", as a parameter and I want to copy it to an VM (parameter2) "C:\TestingSources\Test1\File1.dll" (another parameter3), what Copy-vmguestfile does, it's creating on VM folder in that location with the name of the file, and then puts the file in it it looks like "File1.dll\File1.dll", so when i have many files to copy I've got then folder File2.dll with File2.dll inside (File2.dll\File2.dll), fodler File3.dll with File3.dll inside (file3.dll\file3.dll) and so on.
I hope it's understandable what i just wrote 
if not then i will try and provide some screenshots