Polycaprolactone (PCL) is a widely utilized bioresorbable polymer in tissue engineering applications. However, the absence of intrinsic functional groups in the polymer backbone necessitates the incorporation of functional chemistries to enable the further addition of bioactive molecules to PCL-based surfaces and scaffolds. The current study aimed to incorporate two different functional groups, amine and carboxylate, first on two-dimensional (2D) spin-coated PCL films and, thereafter, throughout all surfaces within three-dimensional (3D) porous PCL-based scaffolds, produced using the thermally induced phase separation (TIPS) method, but in a spatially separated manner. Specifically, gamma irradiation induced grafting of acrylic acid (AA) and 2-aminoethyl methacrylate hydrochloride (AEMA) onto PCL was performed in selected solvents and the resulting substrates were characterized using X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), and contact angle measurements to determine the surface free energy. Results demonstrated that stepwise graft copolymerization of AEMA and AA allows the fabrication of dual-functional surfaces, with chemistry depending on the order of grafting of the two monomers. In addition, 3D scaffolds could be decorated exclusively with carboxylate groups in the interior, while the outer surface displayed dual-functionality. This simple surface modification methodology, with the ability to create spatially separated surface functional groups throughout 3D porous scaffolds post their fabrication, has the potential to be applied to many current and future scaffold systems being investigated in the field of tissue engineering.