A pattern clean-up for fabrication of patterned media using a forced assembly of molecules is disclosed. E-beam lithography is initially used to write the initial patterned bit media structures, which have size and positioning errors. Nano-sized protein molecules are then forced to assemble of on top of the bits. The protein molecules have a very uniform size distribution and assemble into a lattice structure above the e-beam patterned areas. The protein molecules reduce the size and position errors in e-beam patterned structures. This process cleans the signal from the e-beam lithography and lowers the noise in the magnetic reading and writing. This process may be used to fabricate patterned bit media directly on hard disk, or to create a nano-imprint master for mass production of patterned bit media disks.