The FeatureBuilderScratch.gdb database contains the geometries that are output from functions. The database consists of a dataset that contains a grouped layer for topology errors and individual feature classes for point, polyline, and polygon features. The database is saved in a temporary folder in your <Install Location>\Documents and Settings\<User Name>\Local Settings\Temp directory.
The database cumulatively stores the geometries you create, and since there is only one, you can accumulate several geometries over time. To minimize the number of geometries in the database, you can delete them during edit sessions or clear all the features in the Feature Builder Scratch dataset.