No, there is no way to remove them. Blur them, yes, remove. NO.
The reason is that the watermark is burned into the movie itself, thus making it part of the actual video. So, blurring is all that can be done.
You can try the DeLogo filter for VirtualDub/NanDub.
Like previous poster mentioned, it would blur/blend, not really remove it, but if the mark is small enough or in a fairly uniform area, it should be fairly inconspicuous.