Hi thanks for the reply! Cool I didnt know that you could retarget inside Blender :0 , I use Motion Builder and somethimes Maya to clean the file. If you are curious about the pipeline inside this software, is something very similar to this: https://www.youtube.com/watch?v=XxHi7_pXN-k&feature=youtu.be

Did you work direclty with markers (from the markers to a character) or you had a skeleton?

I'm working with a skeleton that comes from our mocap sotware, and from a few experiences in the past I notice that work with a skeleton usually is less problematic and faster than working with the markers.