In this paper, an in situ technique is developed to measure the temperature distribution during the ultrafast laser scribing (machining) of heterogeneous materials using embedded sensors. The materials investigated in this study are an epoxy molding compound (EMC), solder bumps, and a specially designed ultrathin printed circuit board (PCB). The laser machining processes involved in this study are cutting/scribing through EMC and PCB, and trenching/scribing through EMC alone. Small thermocouples have been designed and inserted inside the heterogeneous materials to record the in situ temperature distribution during ultrafast laser irradiation and the thermal effect is carefully investigated. The highest temperature of 100.94 °C is recorded at the corner scribing position. For comparison, a forward-looking infrared (FLIR) thermal imaging camera was applied to capture the real-time surface temperature distributions of PCB and EMC. Owing to the ambient heat radiation, material emissivity, and reflective apparent temperature, the peak surface temperature detected by FLIR would be slightly lower than the in situ temperature measured by an embedded sensor. The thermal design in this jam-packed area is then applied to a standard laser manufacturing process.