The ability to form targeted vascular occlusions in small vessels of the brain is an important technique for studying the microscopic basis of cerebral ischemia. We describe two complementary methods that enable targeted occlusion of any single blood vessel within the upper 500 µm of adult rodent neocortex. Our goal is to generate highly localized regions of ischemia by blocking penetrating arterioles and ascending venules, which are bottlenecks of flow in the cortical angioarchitecture. One method, termed photothrombosis, makes use of linear optical absorption by a photosensitizer, transiently circulated in the blood stream, to induce a clot in a surface or near-surface segment of a vessel. The second method, termed plasma-mediated ablation, makes use of nonlinear optical interactions, without the need to introduce an exogenous absorber, to induce clots in subsurface segments of penetrating vessels, as well as subsurface microvessels and capillaries. The choice of the method for occlusion of individual vessels depends on the location of the vessels being studied and the objectives of the study. Here we describe concurrent high resolution in vivo imaging and auxiliary laser setups, occlusion protocols, and post hoc histological procedures.