Polycrystalline Ni-based superalloys for aerospace and power generation applications are often precipitation hardened to achieve strengthening at elevated temperatures. Here, atom probe microscopy has become an essential tool to study the complex morphology of nanoscale precipitates. This study focuses on Alloy 718, which is hardened by semi-coherent, ordered γ′ (Ni3(Al, Ti)) and γ″ (Ni3(Nb)) particles. According to previous research, these particles often occur as duplets or triplets with a stacking sequence dependent on prior processing. This creates various interfaces with a strong impact on the mechanical properties, highlighting the importance of quantitative studies which are challenging with electron microscopy. We present atom probe data reconstruction and analysis approaches particularly suited for precipitation hardened superalloys. While voltage atom probe allows for an accurate reconstruction, the acquired data volume is often limited. Laser-assisted atom probe provides statistically significant data, but the loss of crystallographic information requires correlation with voltage-mode datasets. We further describe an advanced iso-surface method where initially arbitrarily chosen concentration thresholds of Al + Ti for γ′ and Nb for γ″ particles are optimized. Recognizing the importance of the precipitate stacking order, the different types of precipitate interfaces are quantified, and these methods may be applicable to other engineering alloys.