Molecular templates are effective for inducing the formation of functional organic molecular structures on solid surfaces. Various surface nanopatterns as molecular templates were developed by self-assembly and molecular engineering. These molecular templates were used and led to the formation of ordered assembly of alien species into designed two-dimensional matrices targeting at future applications. Both molecular template and so-fabricated nanopatterned assembly were clearly observed by scanning tunneling microscopy (STM). This paper summarizes some recent results on molecular templates for controlling and ordering organic molecules on solid surfaces mainly from our group. Several typical molecular templates and the consequent nanofabrication of ordered assemblies are described, including template design and fabrication, molecule ordering and patterning with the template as well as the possible application of these systems.