A system and method for determining precisely in-situ the endpoint of halogen-assisted charged particle beam milling of a hole or trench in the backside of the substrate of a flipchip packaged IC. The backside of the IC is mechanically thinned. Optionally, a coarse trench is then milled in the thinned backside of the IC using either laser chemical etching or halogen-assisted charged particle beam milling. A further small trench is milled using a halogen-assisted charged-particle beam (electron or ion beam). The endpoint for milling this small trench is determined precisely by monitoring the power supply leakage current of the IC induced by electron-hole pairs created by the milling process. A precise in-situ endpoint detection signal is generated by modulating the beam at a reference frequency and then amplifying that frequency component in the power supply leakage current with an amplifier, narrow-band amplifier or lock-in amplifier. The precise, in-situ, endpoint signal is processed and displayed for manual or automatic precise in-situ endpoint detection. This approach avoids or minimizes unintentional damage or perturbation of the active diffusion regions in the IC. A range of further operations on the IC can then be performed.