Advances in the particle accelerator technology have enabled numerous fundamental discoveries in 20th century physics. Extensive interdisciplinary research has always supported further development of accelerator technology in efforts of reaching each new energy frontier. Accelerating cavities, which are used to transfer energy to accelerated charged particles, have been one of the main focuses of research and development in the particle accelerator field. Over the last fifty years, in the race to break energy barriers, there has been constant improvement of the maximum stable accelerating field achieved in accelerating cavities. Every increase in the maximum attainable accelerating fields allowed for higher energy upgrades of existing accelerators and more compact designs of new accelerators. Each new and improved technology was faced with ever emerging limiting factors. With the standard high accelerating gradients of more than 25 MV/m, free electrons inside the cavities get accelerated by the field, gaining enough energy to produce more electrons in their interactions with the walls of the cavity. The electron production is exponential and the electron energy transfer to the walls of a cavity can trigger detrimental processes, limiting the performance of the cavity. The root cause of the free electron number gain is a phenomenon called Secondary Electron Emission (SEE). Even though the phenomenon has been known and studied over a century, there are still no effective means of controlling it. The ratio between the 1 Jefferson Laboratory is operated by Jefferson Science Associates under DOE Contract No. DE-AC05-06OR23177. viii NOMENCLATURE SEE Secondary electron emission SEY Secondary electron yield SRF Superconducting radio frequency Tc Critical temperature for superconductivity RRR Residual resistivity ratio Eacc Accelerating gradient Vacc Accelerating voltage d Length of the cavity Q0 Intrinsic quality factor ω Angular resonant frequency U Energy stored by electromagnetic field Pc Dissipated power rf radiofrequency BCP Buffered chemical polishing ECP Electro-chemical polishing HPR High pressure rinsing SEM Scanning electron microscope δ SEY δmax Maximum SEY E0 Primary electron energy E0I Primary electron energy of the first crossover point E0II Primary electron energy of the second crossover point ix E0max Primary electron energy at maximum SEY EDC Energy distribution curve θ Incident angle of the primary electrons WZ Weld zone HAZ Heat affected zone BASE Base metal surface, sample set R-HAZ Heat treated base metal surface WELD Sample set OFFSET Sample set ip Primary electron beam current is Sample current ic Collector current XPS X-ray photoelectron spectroscopy RGA Residual gas analyzer SIMS Secondary ion mass spectroscopy (x), (y), (z) Translational axes of motion R(y) Rotational motion around (y) axis GUI Graphical user interface Uc Collector bias voltage Us Sample bias voltage PBC Primary beam collector iBP Current of the back plate iFP Current of the front plate x A Ratio of the iBP, and sum of the iBP a...