A system comprising: a simulation processing component including at least one processor; a manipulator arm connected to a surgical instrument, wherein the manipulator arm is positioned in a simulation area relative to a physical surgical site an anatomical model, at the physical surgical site, comprising a plurality of ports with each port configured to receive at least one of a cannula or the surgical instrument; (132, 134) and at least one sensor located at the anatomical model or the manipulator arm,, or both, the at least one sensor operative to output sensor signals to the simulation processing component indicative of a position of the surgical instrument (132, 134) or a position of the cannula relative to the anatomical model,, wherein the simulation processing component is configured to perform operations in a simulated setup procedure, the operations in the simulated setup procedure comprising: determining a position of the manipulator arm relative to the physical surgical site, wherein the position of the manipulator arm is provided by a user; determining a position of the anatomical model relative to the manipulator arm by using a registration technique; receiving user selection of one of the plurality of ports by determining the position of the surgical instrument or the position of the cannula relative to the anatomical model based on the output sensor signals of the at least one sensor; and causing output of setup feedback information by a first output device based on a result of the determining of the position of the surgical instrument or the position of the cannula relative to the anatomical model indicating an evaluation of the port selection; and wherein the simulation processing component is configured to perform operations in a simulated surgical procedure based on a resulting position of the manipulator arm resulting from the simulated setup procedure, the operations in the simulated surgical procedure comprising: causing an output of surgical feedback information by the first output device to indicate whether there was an incorrect setup performed during the simulated setup procedure due to an incorrect port selection and indicate an effect of the incorrect setup on the simulated surgical procedure. a simulation processing component including at least one processor; a manipulator arm connected to a surgical instrument, wherein the manipulator arm is positioned in a simulation area relative to a physical surgical site an anatomical model, at the physical surgical site, comprising a plurality of ports with each port configured to receive at least one of a cannula or the surgical instrument; (132, 134) and at least one sensor located at the anatomical model or the manipulator arm,, or both, the at least one sensor operative to output sensor signals to the simulation processing component indicative of a position of the surgical instrument (132, 134) or a position of the cannula relative to the anatomical model,, wherein the simulation processing component is configured to perform operations in a simulated setup procedure, the operations in the simulated setup procedure comprising: determining a position of the manipulator arm relative to the physical surgical site, wherein the position of the manipulator arm is provided by a user; determining a position of the anatomical model relative to the manipulator arm by using a registration technique; determining a position of the manipulator arm relative to the physical surgical site, wherein the position of the manipulator arm is provided by a user; determining a position of the anatomical model relative to the manipulator arm by using a registration technique; receiving user selection of one of the plurality of ports by determining the position of the surgical instrument or the position of the cannula relative to the anatomical model based on the output sensor signals of the at least one sensor; and causing output of setup feedback information by a first output device based on a result of the determining of the position of the surgical instrument or the position of the cannula relative to the anatomical model indicating an evaluation of the port selection; and wherein the simulation processing component is configured to perform operations in a simulated surgical procedure based on a resulting position of the manipulator arm resulting from the simulated setup procedure, the operations in the simulated surgical procedure comprising: causing an output of surgical feedback information by the first output device to indicate whether there was an incorrect setup performed during the simulated setup procedure due to an incorrect port selection and indicate an effect of the incorrect setup on the simulated surgical procedure.