The Maya user guide for modify>replace objects and the digital tutors tutorial below were very useful in figuring out how to replace objects with higher detail instances and reduce the overall number of polygons in the scene.
I thought I’d easily be able to select and replace areas of Matthew’s model but the transforms were frozen so I had to place a locator at the center of each sphere to be replaced instead (I tried searching for recovering transforms or world position but no luck). This was made easier by snapping the ‘locator’ pivot to the ‘local rotation axis’ pivot of each sphere in the model which I found out how to do here:
Pivot to pivot snapping: http://simplymaya.com/forum/showthread.php?t=33926.
This would have been a lot more difficult without been able to make buttons on the custom shelf for ‘center pivot’ and ‘display local rotation axes’ as I had to do it for 80 spheres. If we had of foreseen this problem at the start it would have been much easier to insert the locators by ‘duplicating with transform’ straight up before the model was twisted (the model started as a ladder and was twisted into a double helix). It was also useful been able to select geometry with a particular material.