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If you show some code, we may be able to tell you how to improve it, like using buffered streams for input and output, using better buffer sizes, reading the file only once and writing it multiple times (if the file size is somehow predictable and reasonable), etc. You may also experiment with File.renameTo(), which probably delegates more of the work to the OS (but read carefully the documentation for that method).
Probably most of the multithrrading is pointless if not actually counterproduuctive. There's only one disk: it's not multithreaded.