Once enough filament has been made to print a desired part, shut off the extruder. From here the filament can either be spooled or feed directly into the 3D printer.
You can reuse old spools for your new filament! Most spools have a small hole near the inside. Guide the filament through and either hand spool or use a drill to build your own spooler.
Handspooling filament can be a lengthy process depending on the amount of filament. Patience is key here, don't try to rush through spooling, as it could introduce knots, kinks and other elements that could damage the filament.