This article presents an experimental procedure to perform highly localized compression tests on nanoscale structures/features, such as nanospheres and nanopillars, via standard nanoindentation equipment. Current manufacturing capabilities, such as focused ion beam (FIB), lend themselves well to the creation of micron-spaced nanostructures, but it is fundamental to target an individual instance with little or no damage to the surrounding ones. The procedure successfully addresses the problem of locating and testing purposely designed nanostructures of order of 50 nm or less. The technique is illustrated for the case of closely spaced arrays of nanopillars, which were successfully manufactured, characterized, and tested through several pieces of equipment. For the purposes of compression, along with a traditional Berkovich tip, a new multifunctional (MF) tip was devised. This last tip is endowed with a complex contact geometry enabling both atomic force microscope (AFM) scanning and flat punch compression of the nanostructure. The levels of accuracy in tip positioning as well as robustness to alignment errors are unprecedented in comparison with previous in situ compression tests. As a consequence, the MF tip becomes a versatile tool that can be used beyond uniform compression. As an example, ancillary shear tests in controlled conditions are reported. Such results may lay the bases for metal-forming processes at the nanoscale, such as nanoforging or cutting operations, which are relevant to MEMS design and manufacturing.