An automatic filter changer that automatically inserts and removes a filter from a fluidic path. Filters are introduced into the automatic filter changer in stacks. The lead filter and each stack is removed from its respective stack one by one by a filter separator. The separated filters are deposited onto a shuttle plate which moves the filters into their respective fluidic paths. Fluid couplers connect to each filter to complete their respective fluidic paths and allow fluids to be filtered before sampling. Once collection of the samples is complete, the filters are removed from the fluidic path and discarded or saved for reuse. The shuttle path is returned to its original position to receive new filters to repeat the process again. A graphic user interface is provided to allow the user to program a specific set of instructions to automate the entire process.