Videomerge is designed to remove an evenly-colored background (usually a blue screen or green screen) from a scene shot in a studio -- similar to Chroma Key.
Is this what you're trying to do?
If not, can you post a screen capture of the scenes you're trying to merge together and describe how you're trying to combine them?
Thanks Steve for your reply. I had no green or blue screen involved, so knew I was likely to struggle to achieve the desired outcome. Currently working the scenes through AE CS6 to see if that allows me to make it work. Need to study up on the basics a bit more though. cheers.