Apparatus and methods are described for isolating or manipulating a portion of a sample at non-ambient temperatures and pressures. One apparatus embodiment of the invention comprises a primary sample containment vessel defining a primary chamber, the vessel having a primary sample inlet and outlet; a secondary sample collection container defining a collection chamber fluidly connected to the primary containment vessel; and a sample probe comprising a distal end able to isolate a secondary sample in the primary chamber and transfer it to the collection chamber, the probe fluidly connected to the primary chamber via a seal allowing at least the distal end to be moved in 3-dimensions within the primary chamber. This abstract complies with rules requiring an abstract. It should not be used to limit the scope or meaning of the claims.