The increasing use of flip-chip packaging is challenging the ability of conventional Focused Ion Beam (FIB) systems to perform even the most basic device modification and debug work. The inability to access the front side of the circuit has severely reduced the usefulness of traditional micro-surgery. Advancements in FIB technology and its application now allow access to the circuitry from the backside through the bulk silicon. In order to overcome the problem of imaging through thick silicon, a microscope with Infra Red (IR) capability has been integrated into the FIB system. Navigation can now be achieved using the IR microscope in conjunction with CAD. The integration of a laser interferometer stage enables blind navigation and milling with sub-micron accuracy. To optimize the process, some sample preparation is recommended. Thinning the sample to a thickness of about 100 µm to 200 µm is ideal. Once the sample is thinned, it is then dated in the FIB and the area of interest is identified using the IR microscope. A large hole is milled using the FIB to remove most of the silicon covering the area of interest. At this point the application is very similar to more traditional FIB usage since there is a small amount of silicon to be removed in order to expose a node, cut it or reconnect it. The main differences from front-side applications are that the material being milled is conductive silicon (instead of dielectric) and its feature-less and therefore invisible to a scanned ion beam. In this paper we discuss in detail the method of back-side micro-surgery and its electron device performance. Failure Analysis (FA) is another area that has been severely limited by flip-chip packaging. Localized thinning of the bulk silicon using FIB technology offers access to diagnosing failures in flip-chip assembled parts.