Often hole size can help in identification. A hole 3 to 4 inches in diameter (measured from top to bottom, not side to side) may be a skunk. Woodchuck dens tend to be larger. Rat burrows will be 2 to 3 inches. Chipmunk holes will be 1.5 inches with no dirt on the outside. A lot depends on the soil texture, how long the hole has been used, and whether multiple species have used it.
Regardless of which animal made the tracks, you want to be sure it has left before permanently closing the hole. If the entry has been there for a while, you also need to be sure you are not blocking the mother out while there are still young animals under the house.
Some recommend using talcum powder or flour sprinkled before the entrance to help identify the tracks. Use handbooks available at bookstores, or check track guides online, to match the tracks you see in the powder or flour. Watch the hole to make sure it isn't the entrance to a bees' nest!
To see if the animal is still present, wad up some newspaper, and cork (not fill) the hole with the paper. Monitor the hole. If it is summer and spring time, the newspaper should be moved after several days (assuming weather is good). If not, the hole may be abandoned. Lightly backfill the hole with some loose dirt. Continue to monitor. If there is no more activity, you can probably be reasonably assured that the hole isn't active any more.
Wildlife Damage Inspection Tips