I actually agree with the replies that were made (sorry, Cloneone1. >.<). This question is a hypothetical one. Thoughts are simply electrical pulses created by the brain that differ from eachother, which is why we think. If our brains were to cease function, there would be no more electrical impulses, and therefore our thoughts would stop. Thoughts are not matter. They are basically processes, like a computer. If a computer processor is shut down, there are no electrical pulses nor a current running through it. Therefore, it would cease to "process" things. Without an input and a power source, it doesn't have any use (data = input, power source = electricity).
Same with the human brain. Input is everything that is taken in by the senses. Power source is the body's chemical energy.
Simply put, thoughts = electrical pulses/bioelectricity in the brain. Kill the brain, you kill the thoughts. Done.
Listen, Cloneone1. Your questions might have an underlying meaning that can be discussed somewhat thoroughly, but you should look at it from the logical/scientific point of view. If it can be solved quickly using logic and by the teachings of science, then it's a stupid question (and Hyde will probably close your thread).