We describe a patterned surface-enhanced Raman spectroscopy (SERS) substrate with the ability to pre-concentrate target molecules. A surface-adsorbed nanosphere monolayer can serve two different functions. First, it can be made into a SERS platform when covered by silver. Alternatively, it can be fashioned into a superhydrophobic surface when coated with a hydrophobic molecular species such as decyltrimethoxy silane (DCTMS). Thus, if silver is patterned onto a latter type of substrate, a SERS spot surrounded by a superhydrophobic surface can be prepared. When an aqueous sample is placed on it and allowed to dry, target molecules in the sample become pre-concentrated. We demonstrate the utility of the patterned SERS substrate by evaluating the effects of inhibitors to acetylcholinesterase (AChE). AChE is a popular target for drugs and pesticides because it plays a critical role in nerve signal transduction. We monitored the enzymatic activity of AChE through the SERS spectrum of thiocholine (TC), the end product from acetylthiocholine (ATC). Inhibitory effects of paraoxon and carbaryl on AChE were evaluated from the TC peak intensity. We show that the patterned SERS substrate can reduce both the necessary volumes and concentrations of the enzyme and substrate by a few orders of magnitude in comparison to a non-patterned SERS substrate and the conventional colorimetric method.