Pre-filters prevent airborne particles such as dust and small insects from clogging up the micro and mesopores in the carbon. Keeping pre-filters clean will also maximise airflow through the filter, making sure your area is adequately ventilated at all times. As well as dust and dirt, high humidity can also shorten the lifespan of your carbon filter, so maintaining the desired airflow is important.
Keeping a spare pre-filter handy to swap out with dirty ones is a good idea. If required, you can clean your dirty pre-filters with water and hang them to dry.