Current methods for murine brain microvasculature isolation requires the pooling of brain cortices while disregarding the rest of the CNS, making the analysis of single individuals non feasible. Efficient isolation of brain microvessels requires the elimination of meninges, vessels of high caliber vessels and choroid plexus, commonly done by rolling the over filter paper, but can't be done on other CNS regions. We overcome this hurdle by using a double-pronged pick, as well as elution and filtration through cell strainers after centrifugation. We were able to develop a region-specific murine CNS microvessels isolation, that allows for the comparison of the neurovascular unit from these regions both within the same individual and between multiple individuals and/or treatment groups without pooling. Additionally, we were able to adapt this method to macaque CNS tissue. Although similar to a previously published method that requires no enzymatic dissociation and no ultracentrifugation, it does differ in its ability to isolate from a single experimental animal and from non-cortical tissues. However, it relies heavily on the researcher dissecting skills and careful elution and filtration of re-suspended samples. CNS region-specific microvessels comparison can inform of molecular and/or cellular differences that would otherwise be obscured by excluding non-cortical tissue. Additionally, it allows for the unmasking of variations between individuals that remained hidden when pooling of multiple samples is the norm. Lastly, isolation of region-specific microvessels for non-human primate CNS allows for more translationally relevant studies of the BBB.