Patients with paralysis, spinal cord injury, or amputated limbs could benefit from using brain–machine interface technology for communication and neurorehabilitation. In this study, a 32-channel three-dimensional (3D) multielectrode probe array was developed for the neural interface system of a brain–machine interface to monitor neural activity. A novel microassembly technique involving lead transfer was used to prevent misalignment in the bonding plane during the orthogonal assembly of the 3D multielectrode probe array. Standard microassembly and biopackaging processes were utilized to implement the proposed lead transfer technique. The maximum profile of the integrated 3D neural device was set to 0.50 mm above the pia mater to reduce trauma to brain cells. Benchtop tests characterized the electrical impedance of the neural device. A characterization test revealed that the impedance of the 3D multielectrode probe array was on average approximately 0.55 MΩ at a frequency of 1 KHz. Moreover, in vitro cytotoxicity tests verified the biocompatibility of the device. Subsequently, 3D multielectrode probe arrays were implanted in rats and exhibited the capability to record local field potentials and spike signals.