We present the synthesis of discrete functionalized polyester nanoparticles in selected nanoscale size dimensions via a controlled intermolecular chain cross-linking process. The novel technique involves the controlled coupling of epoxide functionalized polyesters with 2,2'-(ethylenedioxy)bis(ethylamine) to give well-defined nanoparticles with narrow size distribution and selected nanoscopic size dimensions. Diverse functionalized polyesters, synthesized with pendant functionalities via ring-opening copolymerization of delta-valerolactone with alpha-allyl-delta-valerolactone, alpha-propargyl-delta-valerolactone and 2-oxepane-1,5-dione, were prepared as linear precursors which facilitated 3-D nanoparticles with functionalities such as amines, keto groups, and alkynes for post modification reactions. We found that the nanoparticle formation and the control over the nanoscopic dimension is primarily influenced by the degree of the epoxide entity implemented in the precursor polymers and the amount of 2,2'-(ethylenedioxy)bis(ethylamine) as cross-linking reagent. The other functionalities in the linear polyester do not participate in the nanoparticle formation and particles with defined functionalities can be prepared from batches of identical linear polymers containing various functionalities or by mixing different polyester materials to achieve controlled amounts of specific functional groups. The utilization of integrated functionalities was demonstrated in one post-modification reaction with N-Boc-ethylenediamine via reductive amination. This work describes the development of a novel methodology to prepare functionalized well-defined 3-D nanoparticle polyester materials in targeted nanoscopic ranges with amorphous morphologies or tailored crystallinities that offer a multitude of utilizations as a result of their unique properties and control in preparation.