A lot depends on the Trojan, some can be easily removed by Malawarebytes, and others can be very persistent and require hours of tracking through the registry. There are some cleaners that run from a Linux bootable cd/dvd. Unless its like a W8 laptop that I recently dealt with, where the bios was messed around with so that it was difficult to do. (Bloody Asus and MS
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Or do as i had to do in the end, roll back the puter using system restore to go back a day before the problem started.