Biocompatible solvents, systems, apparatus and methods are provided for treating atherosclerosis, heart disease and stroke by dissolving and reducing arterial plaque within a patients cardiovascular system. A biocompatible solvent is described based on desired solubility parameters and molecules of free fatty acids and other compositions which are known to be safe for humans have been identified which meet the required criteria. Furthermore, the physiological implications of injecting the biocompatible solvents into a patient intravenously are considered and the interaction with blood proteins discussed and considered. Finally, a system and apparatus to inject the biocompatible solvents into a patient as well as to filter and remove the solvent from the patients cardiovascular system post injection are described.