The paper reports the methods of preparing molecular magnets and pattering of the molecules on semiconductor surface. A highly magnetically aligned metallothionein containing Mn and Cd (Mn,Cd-MT-2) was first synthesized. Those molecules were then placed into nanopores prepared on silicon (001) surfaces using electron beam lithography and reactive ion etching techniques. We have observed self-assemble growth of those MT molecules on the patterned Si surface. The MT molecules have grown into rod or ring type nanostructures, depending on the patterned nanostructures on the surface. We also provide scanning electron microscopy (SEM) and atomic force microscopy (AFM) studied of those molecular nanostructures. This engineered molecule shows molecular magnetization and is biocompatible with conventional semiconductors. These features make Mn,Cd-MT-2 a good candidate for biological applications and sensing sources of new nano-devices.