I've got a current implementation that works using BG and r-tree but it's using an AABB that completely encompass the query area so I've got a lot of false positives to weed through.  I'm looking for a cleaner way to query a large data set.

The data set consists of X/Y plane squares of various sizes and at various  coordinates within a known range.  The tricky part is that I need to cull all but those that touch a small square area projected along a non-axis aligned vector.

Is there any way to query the r-tree with a non-axis aligned bounding box?  If not is there a known way to do this query that I'm just overlooking?