Many models of physics beyond the Standard Model (SM) contain enhanced couplings to third generation particles. The predicted signatures include vector-like quarks and $t\bar{t}$ resonances. We present a review of non-SUSY based searches for new physics beyond the SM in final states with third-generation quarks using proton-proton collision data collected with the CMS detector at the CERN LHC. We analyze a wide range of final states, from multi-leptonic to entirely hadronic, and many results use novel analysis techniques to identify and reconstruct highly boosted final states that are created in these topologies. These techniques provide increased sensitivity to new high-mass particles over traditional search methods.