How does Matter energy transport function in Star Trek?

I mean, when i played star trek voyager: elite force, when going through the transporter, i see the blue thing around me, but if matter is all broken down this is impossible right??? Unless i don't understand how the transporter works. what Im asking is, will someone who goes through a transporter and see whats going on when they are still materializing or dematerializing? I know such technology does not exits, but in the star trek universe, does it work that way?

This is probably not the best place to ask this question. I would presume, however, that you would see the blue glow (as all scifi tech seems to glow) just before the breakdown effect got to your brain.

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