GISquirrel tables have a spatial index to optimize drawing and other spatial operations. When first imported, this index covers the extent of features contained within the feature class.

In PostGIS, this index is self-maintaining when the layer is edited. In SQL Server, when new features are added that fall significantly outside this extent, GISquirrel allows the user to re-build the index to the cover the new extents. The spatial index can also be managed using the SQL Server Management Studio tools.