Yes, WooCommerce Product Filters works with all brand plugins such as WooCommerce Brands. The brand information in these plugins is stored as a custom taxonomy, so you can create a taxonomy filter to allow customers to filter by brand.
Alternatively, you can create your own 'Brands' custom taxonomy using our free Easy Post Types and Fields plugin. This saves buying a separate WooCommerce brands plugin. Just install the free plugin, go to Post Types → Other Post Types, choose the 'Products' post type and add a custom taxonomy called 'Brand' to this. You can then add a brand to each product and use WooCommerce Product Filters to create a filter by brand.