A method for preparing surgical kits for use during a surgery includes preparing a pre-operative surgical plan for a patient and selecting a set of surgical instruments based on the pre-operative surgical plan. The set of surgical instruments includes at least a general instrument, a first size-specific instrument, a patient-specific instrument, and a surgeon-specific instrument. The general instrument is selected from a predetermined group of off-the-shelf instruments. The first size-specific instrument has a first size selected from predetermined sizes. The patient-specific instrument includes a three-dimensional contoured engagement surface configured to nest into a portion of a native anatomy in a single location. The surgeon-specific instrument is selected based on a surgeon preference and is a different instrument than the selected general instrument, first size-specific instrument, and patient-specific instrument. The method further includes preparing a surgeon instrument kit containing the set of surgical instruments in sterilized form.