I have a file which has a watermark which appears at certain time throughout. Is it possible to apply a blur at these certain times?
If it's an AVI, VirtualDub can get it done. The overall video quality will take a hit, though, because you'll have to re-encode.
Try the logoaway filter in Virtualdub. http://www.videohelp.com/tools/Virtualdub_Logoaway_filter Setup multiple instances of the filter corresponding to all the different positions the logo occupies. Activate Blend mode for all instances, and turn on the Curve Editor. Using the editor, select each instance of the filter and the frame range(es) where it should be active. Might take a while to set up, but it should work. I tested it myself and chose the UGLARM mode of the filter.