General control of atoms and molecules has long been a goal for atomic physicists and physical chemists. Techniques such as laser cooling have been a huge breakthrough in studying ultra cold atoms and BECs. Although laser cooling has been a remarkable tool, it is limited to small group of atoms on the periodic table. A general technique to control and manipulate the entire periodic table has been out of reach until now. In this thesis I describe two methods of general control of atoms in the contexts of stopping supersonic beams and of isotope separation. Both these methods take advantage of high flux supersonic beams and the fact that every atom has a magnetic moment in the ground state or a long-lived excited state which can be manipulated using magnetic field gradients. The first method uses a series of pulsed electomagnetic coils to slow and stop a supersonic beam of paramagnetic atoms and molecules. We have demonstrated the slowing of metastable neon and molecular oxygen using 64 coils from 446.5 m/s to 55.8 m/s for metastable neon, and from 389 m/s to 83 m/s for molecular oxygen respectively. The second method is a novel and efficient approach to isotope separation which utilizes the concept of Maxwell's Demon. We call this technique Single-Photon Atomic Sorting as it is closely related to Single-Photon Cooling, a cooling technique developed in our laboratory. Our method uses a laser beam to change the magnetic moment to mass ratio in such a way that the desired isotopes are guided through a multi-pole magnetic field and collected. We show simulation results for various test cases which highlight the general applicability of this method. / text