Abstract: The methods for sample preparation disclosed herein utilize an air phase to reduce aqueous phase associated with magnetic particles bound to nucleic acids to decrease carryover of one or more contaminants, such as, cell debris, chaotropic agents, non-specifically attached molecules, and the like. This air-transfer step is improved by using a combination of a first population of magnetic particles and a second population of magnetic particles, where the first population of magnetic particles is capable of associating with nucleic acids, and the magnetic particles in the second population are at least two-times larger in size than the size of the magnetic particles in the first population. As discussed herein, the use of this second population of magnetic particles improves the transfer of the first population of magnetic particles by reducing loss of the first magnetic particles during the transfer. The sample preparation methods may be semi-automated or completely automated.