Crispin Green is up for an honour in the Editing: Fiction/Entertainment category, while The Mill has been put forward for recognition in the Visual Effects section.
The winners will be announced at a ceremony at The Dorchester hotel in London on April 22.
Last year, the show was nominated for four craft awards but didn't win any, although Mike Tucker, who was in charge of the model effects, was in the team that scooped the gong for Best Visual Effects for the BBC1 drama/documentary Hiroshima.
(Thanks to Neil Marsh.)
POSTSCRIPT: As well as Doctor Who being nominated, The Model Unit, run by Mike Tucker, is also in line for an award for its visual effects work on Krakatoa: The Last Days, while Neill Gorton is nominated, alongside Vanessa White, for make-up and hair design on The Catherine Tate Show.