In this paper, the mechanism of the recently introduced soft lithographic patterning approach of reactive microcontact printing on thin substrate-supported polystyrene-block-poly(tert-butyl acrylate) (PS690-b-PtBA1210) films using trifluoroacetic acid (TFA)-inked elastomeric poly(dimethylsiloxane) (PDMS) stamps is investigated in detail. In this approach, solventless deprotection reactions are carried out with very high spatial definition using TFA as a volatile reagent that partitions into the PtBA skin layer. On the basis of a systematic investigation of the process, ink loading was identified as a crucial parameter for obtaining faithful pattern transfer. Using optimized conditions, submicrometer-sized patterns were successfully fabricated. In combination with subsequent wet chemical covalent coupling of various (bio)molecules, reactive uCP is established as an approach to afford positive, as well as negative, images of the features of the stamps used. In addition, the size of the patterned areas was manipulated by exploiting the controlled spreading of the ink; thus, stamps with identical features yield patterns with different sizes, yet identical periodicity, as shown for bovine serum albumin (BSA)-poly(ethylene glycol) patterns. The reactive uCP methodology affords new pathways for submicrometer-scale patterning of bioreactive surfaces.