An apparatus for the transfer of samples from an analytical instrument has a sealable transfer capsule and a means for connecting the transfer capsule to a vacuum instrument, such as a FIB, through an interface connected to the instrument. The capsule has a door that can be opened to insert a sample holder, such as a TEM sample holder, into the instrument, and then closed when the sample holder holding an excised sample is retracted back into the transfer capsule. The instrument interface contains means for sealing the instrument before the transfer capsule holding a sample is disconnected, and for purging the transfer capsule with an inert gas. The sample may thus be transported in the sealed transfer capsule without exposure to the ambient atmosphere. The sample may be transported to and connected to a glove box also purged with an inert gas for examination or further operations.