This paper demonstrates a facile method to achieve high yield and uniform fabrication for the transfer printing of nanoplasmonic structures on a flexible substrate by providing novel understanding on adhesion layers. The mercapto alkyl carboxylic acids and the alkyl dithiols are used as functionalized adhesion layers and further optimized by controlling the terminal group as well as the length and composition of the functionalization on flat and nanostructured gold surfaces. Our approach of optimized adhesion has been successfully implemented to the transfer printing of functionalized gold nanostructure arrays, thus producing much higher yield of 97.6% and uniform fabrication of nanostructures on a flexible substrate and enabling applications such as flexible nanoplasmonic devices and biosensing platforms.