The present invention includes compositions and methods of making a modified release pharmaceutical formulation and a method of preparation for the embedding of modified release multi-particulates into a polymeric or wax-like matrix. The modified release multi-particulates comprise an effective amount of a therapeutic compound having a known or desired drug-release profile. Modified release multi-particulates may include a polymeric coat or may be incorporated into particle or core material. The polymer matrix comprises a thermoplastic polymer or lipophilic carrier or a mixture thereof that softens or melts at elevated temperature and allows the distribution of the modified release multi-particulates in the polymer matrix during thermal processing. Formulation compounds and processing conditions are selected in a manner to preserve the controlled release characteristics and/or drug-protective properties of the original modified release multi-particulates.