The disclosed technology provides for printing a 3D structure in-situ within a patient during a surgical procedure. The disclosed technology can include generating instructions for a 3D printer of a surgical robot to print a structure within the patient's body, simulating and verifying the instructions, and autonomously or semi-autonomously executing the instructions, once verified, during a surgical procedure. Generating the instructions for printing the 3D structure within the patient can be based on image data of the patient. Generating the instructions can also include selecting substrate materials that are both safe for the patient and having desired properties of the final printed structure. Modifications can be made to the instructions based on results from the simulation. The disclosed technology provides for application of safe substrate material directly to hard and/or soft tissues within the patient's body via an additive manufacturing process, such as 3D printing.