His early work was as a writer. His scripts included The Man Who Finally Died (1967) for the BBC and Special Branch for Thames Television (1970). He also wrote for Danger Man with Patrick McGoohan, and for the Doomwatch science fiction series and for Doctor Who on four occasions. The first of these, "Planet of Giants", opened the second season of the programme in 1964. Marks is the earliest surviving credited writer of the series and one of only three living writers from the Hartnell era of the programme, the others being Donald Tosh and Glyn Jones. His second script was "Day of the Daleks" in 1972 and as originally written, the serial revolved around the Ogrons instead of the Daleks. During the Tom Baker years he wrote the "Jekyll and Hyde" script for "Planet of Evil"; and then "The Masque of Mandragora", which was perhaps his most unusual script for Doctor Who and drew on his academic background and studies in Renaissance Italy.
Marks' producer credits include The Lost Boys (1978), Fearless Frank (1979), the BBC's adaptation of the Three Theban plays (between 1984 and 1986), and the BBC's adaptation of George Eliot's Middlemarch (1994). He worked with Jack Clayton on an adaption of Muriel Spark's Memento Mori in 1991, Harold Pinter on The Hothouse 1987 and with Mike Leigh on Grown-ups 1982.
He has worked with distinguished actors including Anthony Hopkins, Claire Bloom, John Gielgud, Nigel Hawthorne, Michael Gambon, Judi Dench and Ben Kingsley on the adaptation of another George Eliot work Silas Marner in 1986.