In this study, we fabricated a paper-based molecule-detecting sensor for the surface-enhanced Raman scattering (SERS) technique. SERS phenomenon is based on the face that the low intensity of Raman scattering is dramatically increased when the molecules are adsorbed on novel metal surface. To improve the applicability of paper substrate as a base for SERS several trials were made. The smoothness of the filter paper was improved through a calendaring process. To prevent the spreading of the chemical solution on the aper the hydrophobicity of paper was increased by treating with an alkyl ketene dimer (AKD). Onto the smooth and hydrophobic filter paper a silver nanoparticle (AgNP) solution was applied with a simple drop and dry method, and analyte was treated in the same manner on the AgNP decorated area for SERS measurement. To improve the reproducibility of the SERS intensity, an area scanning method that used a dual axis galvanometric mirror was introduced. A 4-aminothiophenol molecule could be detected at the femtomolar level using the hydrophobic-treated filter paper. Coating of cellulose nanofibrils (CNF) made from pulp fibers reduced the surface pore sizes and increased the uniformity of the surface of the filter paper, which improved the reproducibility and sensitivity of the molecule-detecting sensor. The use of a high magnification objective lens for increased SERS intensity allowed for the detection of a strong SERS signal, and the application of a CNF coating to the filter paper improved the reproducibility. Pesticides were detected using the paper-based substrate as SERS substrate.