Two-dimensional atomic crystals (2DACs) can be mechanically assembled with precision for the fabrication of heterostructures, allowing for the combination of material building blocks with great flexibility. In addition, while conventional nanolithography can be detrimental to most of the 2DACs which are not sufficiently inert, mechanical assembly potentially minimizes the nanofabrication processing and preserves the intrinsic physical properties of the 2DACs. In this work we study the interfacial charge transport between various 2DACs and electrical contacts, by fabricating and characterizing 2DAC-superconductor junctions through mechanical transfer. Compared to devices fabricated with conventional nanolithography, mechanically assembled devices show comparable or better interface transparency. Surface roughness at the electrical contacts is identified to be a major limitation to the interface quality.