A computer-implemented method for radiation therapy treatment planning, the method comprising: receiving, at a computer system, input defining a plurality of regions including a first structure and a second structure and an original treatment objective for each of the regions, the original treatment objectives including a first original treatment objective for the first structure and a second original treatment objective for the second structure, wherein the first original treatment objective is inconsistent with the second original treatment objective; detecting, by the computer system, a geometric overlap between the first structure and the second structure; defining, by the computer system, a margin around the first structure; defining, by the computer system, a plurality of modified regions including: a first modified region that includes any portion of the second structure that does not overlap with the first structure or the margin, a second modified region that includes any portion of the first structure that does not overlap with the second structure, a third modified region that includes any portion of the second structure that overlaps with the margin, and a fourth modified region that includes any portion of the second structure that overlaps with the first structure; characterised by the following steps: determining, by the computer system, a set of modified treatment objectives including a first modified treatment objective for the first modified region, a second modified treatment objective for the second modified region, a third modified treatment objective for the third modified region, and a fourth modified treatment objective for the fourth modified region, wherein the modified treatment objectives are determined based on the first original treatment objective and the second original treatment objective; and using, by the computer system, the plurality of modified regions and the set of modified treatment objectives in a treatment planning process to generate a treatment plan for treating a patient. receiving, at a computer system, input defining a plurality of regions including a first structure and a second structure and an original treatment objective for each of the regions, the original treatment objectives including a first original treatment objective for the first structure and a second original treatment objective for the second structure, wherein the first original treatment objective is inconsistent with the second original treatment objective; detecting, by the computer system, a geometric overlap between the first structure and the second structure; defining, by the computer system, a margin around the first structure; defining, by the computer system, a plurality of modified regions including: a first modified region that includes any portion of the second structure that does not overlap with the first structure or the margin, a second modified region that includes any portion of the first structure that does not overlap with the second structure, a third modified region that includes any portion of the second structure that overlaps with the margin, and a fourth modified region that includes any portion of the second structure that overlaps with the first structure; a first modified region that includes any portion of the second structure that does not overlap with the first structure or the margin, a second modified region that includes any portion of the first structure that does not overlap with the second structure, a third modified region that includes any portion of the second structure that overlaps with the margin, and a fourth modified region that includes any portion of the second structure that overlaps with the first structure; determining, by the computer system, a set of modified treatment objectives including a first modified treatment objective for the first modified region, a second modified treatment objective for the second modified region, a third modified treatment objective for the third modified region, and a fourth modified treatment objective for the fourth modified region, wherein the modified treatment objectives are determined based on the first original treatment objective and the second original treatment objective; and using, by the computer system, the plurality of modified regions and the set of modified treatment objectives in a treatment planning process to generate a treatment plan for treating a patient.