I would like to define the area in which a transformer should be applied by using a polygon mask. I know this can be done in FME but I can´t find any references to it. Can anyone enlighten me?
The SpatialFilter will leave your geometries as they are: geometries that touch your bounding polygon can be left intact.
The Clipper will perform a geometric clip of your features at the edges of the bounding polygon.
If you are dealing with large amounts of data you may want to consider using "Use Search Envelope" on your reader (if available) with your bounding polygon's Max and Min x/y's first, then do your Clipper or SpatialFilter as it should be more efficient.
You could use a Clipper transformer to clip out only the area of data to be processed. Is that what you are looking for? There are very few transformers that accept a polygon as a boundary to the transformation to be completed; in fact the only one I can think of is the FeatureReader transformer.