Hello, superego13itch. Always nice to see new people. I always mean to ask this from newcomers but I always forget, so I'll ask this time: how did you stumble across VGMaps.com?
I'm not familiar with Alien3 on the Genesis, but if it's like most any other 2D game, removing the half-Ripleys and score should be as simple as copying and pasting from other areas of the map or taking a second screenshot in the same area with Ripley in a different position, then pasting together portions of the screenshots without her.
DarkWolf is the resident Genesis guru around here, perhaps he knows some tricks, as he seems able to churn out Genesis maps by taking level data straight from the code rather than working with screenshots.