Osteoporosis is a disease characterized by high fracture risk and low bone mass. Bone mineral density is modified by a process known as bone remodeling. Bone remodeling is the resorption of bone by osteoclasts followed by deposition of new bone by osteoblasts. Because the resorption phase precedes formation, remodeling results in the formation of temporary cavities known as resorption cavities. Resorption cavities act as stress risers and are believed to impair fatigue properties and increase fracture risk. To better understand how bone remodeling affects the biomechanical properties of cancellous bone, images of bone and fluorescent markers of bone formation are collected through serial block face imaging. Images are collected using a computer numerically controlled mill with an attached fluorescence microscope. The techniques described here address factors contributing to imaging imprecision inherent to serial block face imaging using epifluorescence microscopy and allow direct measurement of resorption cavities.