Extractions are generally preferred over filtrations to remove impurities. Extractions can often be performed in the vessel where the reaction occurred, while filtration require additional equipment (filters, receivers and transfer lines) and more operations. Filter elements can also plug, causing delays in processing. For instance, it is more convenient to remove Et3N-HCl from a reaction run in toluene by extraction into water than by filtration; however, if large volumes are needed for extractions, filtration may be preferred. Solvents that dissolve small amounts of water may be preferred if the product is water-sensitive. For instance, i-PrOAc may be preferred over EtOAc.Perhaps the thing that separates laboratory-scale operations from plant-scale operations is the lack of a bottom valve on laboratory flasks*; the bottom valve is what allows a 2000-gallon reactor to serve as its own separatory funnel. Pump the water in, turn on the agitator for a while, let it settle, drain your aqueous layer away, Bob's your uncle.
*Although you can certainly purchase them with bottom valves!