Production
"Per Manum" featured the appearance of David Duchovny as Fox Mulder in various flashbacks. After settling his contract dispute with Fox, Duchovny quit full-time participation in the show after the seventh season. In order to explain Mulder's absence, Duchovny's character was abducted by aliens in the seventh season finale, "Requiem". After several rounds of contractual discussions, Duchovny agreed to return for a total of 11 season eight episodes. "Per Manum" marked the fourth appearance of Duchovny in the eighth season; he had previously appeared in opening episodes of the season, "Within" and "Without" as well as the eleventh episode "The Gift". Series creator Chris Carter later argued that Mulder's absences from the series did not affect the characterization, noting that "there are characters who can be powerful as absent centers, as Mulder was through the eight and ninth seasons."
A deleted scene from early on within the episode, in which Scully questions her doctor about her ultrasound scans, was cut from the final broadcast as writer Frank Spotnitz felt it was too "confusing" for the viewers to place doubt on the actions of the doctor so early. Fellow series writer John Shiban said that the scene was not "subtle" enough to convey the right level of suspicion. Spotnitz has described "Per Manum" as being "a real paranoia episode", concerning "the way you perceive connections between people, what are they saying, and is it suspicious or not".
Adam Baldwin, who makes his first appearance as recurring character Knowle Rohrer, originally auditioned for the part of John Dogget, losing out to Robert Patrick. However, the crew remembered Baldwin's audition later when casting "Per Manum", and asked him to play the role. Jay Acovone, who portrays Duffy Haskel in this episode, returned in the same role in the season's penultimate episode "Essence"; and had also previously appeared in the fourth season episode "Demons". "Per Manum" also featured a guest appearance by Mark Snow as an unnamed doctor. Snow had been the series' composer since the first season.
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