The Northampton manager pulled off something of a coup in landing the 32-year-old defender on loan in January, Carlisle having been playing at the top level as recently as 2010 with Burnley.
Reunited with his former Watford boss the central defender played his part to the full as Town stayed in League Two but Boothroyd knows he faces competition to do a permanent deal.
"Conversations with Clarke are ongoing,” he said.
"I thanked all the loan players on Friday for the work they have done with us. Clarke will have a lot of offers and we’ve got to put an offer together for him and make sure all the little things that are important in his life are right for him."