We report on the results of a parametric optimization of micro-contact printing based thermal transfer of electrospun nanofibers. Fiber electrospinning was performed with a solution of thermoplastic polymer and a collector having a rectangular open area. After electrospinning, a piece of elastomer polydimethylsiloxane (PDMS) was used to scratch nanofibers from the open area and to thermally transfer them to the surface of a glass substrate by micro-contact printing at a temperature slightly higher than the glass transition temperature of the polymer. With the help of optical measurements, we optimized the printing conditions including the temperature and printing duration. Then, the stability of the transferred nanofibers was studied with sonication at different power rates. As expected, the printed nanofibers showed a much enhanced adhesion stability, comparing to the as-deposited nanofibers. Furthermore, the nanofibers after thermal transfer could be used for patterning by using conventional photolithography and reactive ion etch techniques.