In some examples, a method for preparing one or more bones involves inserting a spacer into a space defined between a first bone and a second bone, such as a joint space between a first metatarsal and medial cuneiform. A bone preparation guide can be aligned with opposed ends of the first bone and the second bone using the spacer as an alignment reference. For example, the bone preparation guide may include an opening such that the guide can be installed across the joint space with the spacer received in the opening. A clinician may use the bone preparation guide to guide a tissue removing instrument to cut or otherwise prepare the ends of the first bone portion and second bone portion.