Jessica, Would you be able to share the settings you used? I am attempting something similar - I'm trying to merge polygons less than .5 acres in area into the adjacent polygon. I think I followed John's suggestion about creating a selection and have selected all the small polygons I want to eliminate. The Eliminate tool has been running for over 20 hours and is at the Processing Tiles step for most of that time - progress bar goes to 100%, then cycles back to 23% or so and repeats this pattern over and over. Does this sound familiar? (I am trying to eliminate 13, 000 polygons out of a dataset that has 334,000 polygons. )