If we were actually just pieces of matter we wouldn't be able to actually feel anything as we do. Think about the brain as a very complex computer. It interacts with the world by using sensors which are basically neurons connected to the brain through the nervous system. For every feeling detected (pain, pleasure, the images you constantly see, etc) the brain processes an output. For example, if you put your hand over a fire you will immediately take it out because the brain quickly processed the necessary output based on the pain feeling. The same happens even with your conscious part, which is able to take more complex decisions and isn't based on primitive patterns.

If I can make a computer that mimics how the brain processes feelings, thoughts and emotions, does it mean it can feel like we do? Apparently this has already been made with the brain of a fruit fly. Obviously not.

So, if the brain is just matter, how is it that I can feel instead of just reacting to inputs based on purely physical and logical organic systems?

My theory is this is because we own a soul.