Containers for separating microcarriers from a cell culture fluid that offer a greater efficiency of filtration of cell culture fluids containing microcarriers relative to systems described in the art. The container may include a first compartment that may include a sterile collapsible bag, an inlet port providing a fluid path into the first compartment and an outlet port providing a fluid path exiting the first compartment; and a second compartment fluidly connected with the inlet port of the first compartment and including a plurality of independent or discrete microcarrier receiving regions defined by boundary walls which are partially or fully porous and having a porosity sufficient to retain the microcarriers inside the second compartment, while allowing the cell culture fluid to pass through the second compartment into the outlet port of the first compartment, where the cell culture fluid can be collected.