If the custom fields are stored as product attributes then yes. If the custom fields are stored as postmeta then this is coming in a new feature pretty soon.

There’s a Trello card here: https://trello.com/c/nhTVbEd3/192-fww-add-postmeta-filter

If you can please add comments to that card with examples of the kind of data you wish to filter and how you wish to filter it, that would be very helpful.