They used Softimage|3d for the geometry as well 
Capcom has always been a heavy user of Si3D and XSI. The engine itself would have been one they created.
Of course everything back then in that era of Resident Evil (save for the charactes) were pre-rendered. This means you would either build simple geometry and use a camera to project a matte painting on it, or put as much detail as you need into a scene (but only from the angles the player will see) and use something like Softimage's Rendermap to bake the detail into textures to apply to the simple geometry. Just about any 3d program will do of course
Edited by: Cryrid