We do this two different ways, using polyethylene (PE) molds or aluminum weigh boats, depending on the sample, You can either heat- or UV-cure these molds-just change the type of “lid” on the embedding mold.
The PE molds are used when the coverslip can be made to fit in the mold. We use JB-4-type molds, available from your favorite microscopy supplier. The key to using these molds is that they have to be pre-treated...fill the inner cup of the mold with LR White, cover with an aluminum JB-4 chuck (try to have enough resin in the mold to come up around the base of the chuck), and polymerize in a 60° C oven for a day or two, until the resin is hard.