We'll need to know which version of windows, and if the computer is a brand name (example: HP, Dell, Lenovo, etc).
Most brand name companies install Windows in EFI formatting, meaning that cloning the drives becomes very difficult without the correct software.
I can tell you that the Paragon software works great (Paragon Hard Disk Manager, Paragon Migrate OS, etc) for cloning EFI as it has the option to repair the BCDStore (the partition that contains the Windows Boot information- this is typically destroyed when cloning an EFI install of Windows)
There is one thing you can try if you have a Windows disk (needs to either match the version, or be newer than your Windows):
1. Boot from the Windows Disk
2. When you get to the language selection screen, press Shift+F10 (this will open a command prompt)
3. Type this: bootrec /rebuildbcd
4. Once it's completed, run this to reboot your machine: wpeutil reboot
If it still won't boot, you'll need some special EFI cloning software as there is likely a missing partition.