Recent advances in next-generation sequencing have led to an increased use of formalin-fixed and paraffin-embedded (FFPE) tissues for medical samples in disease and scientific research. Single Molecule, Real-Time (SMRT) Sequencing offers a unique advantage for direct analysis of FFPE samples without amplification. However, obtaining ample long-read information from FFPE samples has been a challenge due to the quality and quantity of the extracted DNA. FFPE samples often contain damaged sites, including breaks in the backbone and missing or altered nucleotide bases, which directly impact sequencing and target enrichment. Additionally, the quality and quantity of the recovered DNA vary depending on the extraction methods used. We have evaluated the Covaris® Adaptive Focused Acoustics (AFA) system as a method for obtaining high molecular weight DNA suitable for SMRTbell™ template preparation and subsequent PacBio RS II sequencing. To test the Covaris system, we extracted DNA from normal kidney FFPE scrolls acquired from the Cooperative Human Tissue Network (CHTN), University of Pennsylvania. Damaged sites in the extracted DNA were repaired using a DNA Damage Repair step, and the treated DNA was constructed into SMRTbell libraries for sequencing on the PacBio System. Using the same repaired DNA, we also tested the efficiency of PCR in amplifying targets of up to 10 kb. The resulting amplicons were also constructed into SMRTbell templates for full-length sequencing on the PacBio System. We found the Adaptive Focused Acoustics (AFA) system by Covaris to be effective. This system is easy and simple to use, and the resulting DNA is compatible with SMRTbell library preparation for targeted and whole genome SMRT Sequencing. The data presented here demonstrates feasibility of SMRT Sequencing with FFPE samples.