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I already know of grass' v.clean, but I'm looking for something that doesn't involve third party software.

Python scripts or addons are good candidates.

What is arcgis eliminate : http://webhelp.esri.com/arcgisdesktop/9.3/index.cfm?TopicName=Eliminate%20(coverage)

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I don't want to "eliminate" sliver polygons. I want to merge small coastal basin with adjutant bigger ones. –  nickves Aug 14 '12 at 12:28
    
I guess you know that the GRASS command v.clean tool=rmarea can be run as a plugin withing QGIS ?? –  Micha Aug 14 '12 at 13:30
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as Micha said the right tool is v.clean or even v.in.ogr from GRASS. As you can use GRASS tools inside QGIS (with the GRASS plugin or with Sextante) you can barely call it a "3rd party software". If you follow the Sextante way you don't even need to understand the GRASS data model, as data are imported and exported on the fly while running a tool. –  Giovanni Manghi Aug 15 '12 at 17:49
    
Did you ever figure out how to perform this "merge" with Grass? I'm losing border area on mine when using Grass' rmarea, I believe similar to what you had happening. –  jocull Apr 10 at 16:44
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