A method of registering a patient's anatomy with an instrument attached to an end-effector of a robotic arm of a robotic surgical system, the method comprising the steps of: attaching a plurality of fiducial markers (3910; 4010a-c; 4110a-b) to the skin of the patient at various locations wherein the fiducial markers are engineered to be visible in intra-operative and/or preoperative imaging so that the positions of the fiducial markers may be automatically identified using image recognition algorithms, each fiducial marker (3910; 4010a-c; 4110a-b) having a hole, receiving, by a processor of a computing device, haptic feedback, from a force sensor, attached directly or indirectly to the robotic arm, prompted by movement of the end-effector; manipulating by the user the instrument to contact a part of each fiducial marker (3910; 4010a-c; 4110a-b) or a portion of the patient's skin identified by the hole in each fiducial marker (3910; 4010a-c; 4110a-b), determining, by the processor, that the haptic feedback corresponds to contact of the instrument with the material of the part of the respective fiducial marker (3910; 4010a-c; 4110a-b) or the portion of the patient's skin identified by the hole in the respective fiducial marker (3910; 4010a-c; 4110a-b) based at least on a magnitude of the haptic feedback exceeding a threshold; determining, by the processor, a set of spatial coordinates, wherein the set of spatial coordinates comprises a spatial coordinate for each contact of the instrument with the part of the respective fiducial marker (3910; 4010a-c; 4110a-b) or the portion of the patient's skin identified by the hole in the respective fiducial marker (3910; 4010a-c; 4110a-b), expressed using a robot coordinate system, wherein each spatial coordinate corresponds to a point on the surface of the patient's anatomy including the fiducial markers (3910; 4010a-c; 4110a-b); receiving, by the processor, a set of medical image data coordinates expressed using a medical image data coordinate system that correspond to the patient's anatomy surface including the fiducial markers (3910; 4010a-c; 4110a-b); mapping, by the processor, the surface corresponding to the set of spatial coordinates to the patient's anatomy surface corresponding to the set of medical image data coordinates; generating, by the processor, a coordinate mapping between the robot coordinate system and the medical image data coordinate system based on the mapping between the surface corresponding to the set of spatial coordinates and the surface corresponding to the set of medical image data coordinates; and storing, by the processor, the coordinate mapping, thereby registering the patient's anatomy to the robotic surgical system. attaching a plurality of fiducial markers (3910; 4010a-c; 4110a-b) to the skin of the patient at various locations wherein the fiducial markers are engineered to be visible in intra-operative and/or preoperative imaging so that the positions of the fiducial markers may be automatically identified using image recognition algorithms, each fiducial marker (3910; 4010a-c; 4110a-b) having a hole, receiving, by a processor of a computing device, haptic feedback, from a force sensor, attached directly or indirectly to the robotic arm, prompted by movement of the end-effector; manipulating by the user the instrument to contact a part of each fiducial marker (3910; 4010a-c; 4110a-b) or a portion of the patient's skin identified by the hole in each fiducial marker (3910; 4010a-c; 4110a-b), determining, by the processor, that the haptic feedback corresponds to contact of the instrument with the material of the part of the respective fiducial marker (3910; 4010a-c; 4110a-b) or the portion of the patient's skin identified by the hole in the respective fiducial marker (3910; 4010a-c; 4110a-b) based at least on a magnitude of the haptic feedback exceeding a threshold; determining, by the processor, a set of spatial coordinates, wherein the set of spatial coordinates comprises a spatial coordinate for each contact of the instrument with the part of the respective fiducial marker (3910; 4010a-c; 4110a-b) or the portion of the patient's skin identified by the hole in the respective fiducial marker (3910; 4010a-c; 4110a-b), expressed using a robot coordinate system, wherein each spatial coordinate corresponds to a point on the surface of the patient's anatomy including the fiducial markers (3910; 4010a-c; 4110a-b); receiving, by the processor, a set of medical image data coordinates expressed using a medical image data coordinate system that correspond to the patient's anatomy surface including the fiducial markers (3910; 4010a-c; 4110a-b); mapping, by the processor, the surface corresponding to the set of spatial coordinates to the patient's anatomy surface corresponding to the set of medical image data coordinates; generating, by the processor, a coordinate mapping between the robot coordinate system and the medical image data coordinate system based on the mapping between the surface corresponding to the set of spatial coordinates and the surface corresponding to the set of medical image data coordinates; and storing, by the processor, the coordinate mapping, thereby registering the patient's anatomy to the robotic surgical system.