Controlling the molecular organization of organic selfassembled monolayers (SAM) is of utmost importance in nanotechnology, molecular electronics, and surface science. Here we propose two well-differentiated approaches, double printing based on microcontact printing (μ-cp) and molecular backfilling adsorption, to produce complex alkanethiol films. The resulting films on model Au surfaces were characterized by atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and contact angle measurements. Double printing alkanethiols results in clear coexisting regions where no molecular displacement is observed, highlighting the slow diffusion rates of long alkanethiols and large attractive interaction between long alkyl chains. Exposing a single-print μ-cp Au substrate to an additional alkanethiol solution yields the formation of differently ordered domain boundaries with different thickness and micrometer lateral size. The high order is a result of enhanced molecular mobility and restructuring during solution backfilling. The formed molecular assemblies constitute an excellent testing ground for nanoscale phenomena that strongly depend on the nanoscale geometrical and chemical features of the surface such as designed functionality or corrosion initiation and inhibition.