yes you can

if you click 'harvest and remove' it will harvest all of t he clay in the deposit and then 'remove' the deposit site, though i would wait before removing it until rain clouds create new deposits in areas that are better suited, as a huge gateway is the ammount of clay you can harvest

found that out hte hard way, spent 3-4 biomes waiting until my '4' deposits had harvested enough clay to research and build the buildings i needed in the first 30 days or so because i removed the other 7

The Harvest Tool has filters that you can set to make this the default too (mainly in situations where you want to mass-select multiple objects, i.e. you can set it so you can select all of Onbu's back and only tag Berry Bushes for removal) - lots of useful options you can experiment with to make management easier ^_^