Methods and devices are provided for preparing and separating biological analytes. In one embodiment, one or more filtration devices or filter plate wells can be formed by clamping a filter sheet between first and second plates having at least one connecting cavity. First and second moveable core pins positioned on opposed sides of the sheet can be moved to remove portions of the sheet. A molten plastic can be injected to fill the volume between the cores and cavities and to form a liquid-impermeable sleeve wall or walls, each being separately sealed at the bottom to the perimeter of the sheet portion, each having liquid permeable regions of said removed and sealed sheet portion, and each remaining open at the top. Various exemplary configurations for filtration devices or filter plate wells are also disclosed.