The company is blaming the cuts in Aberdeen, Glasgow and Witney in Oxfordshire on a downturn in demand.
The firm curently employs 257 people across the UK.
The group said there were 40 proposed redundancies, with a total of 66 posts at risk – 25 in Aberdeen, eight in Glasgow and 33 in Witney.
Stewart Milne Timber Systems managing director Alex Goodfellow told the BBC: “While we have tried as far as possible to minimise the effects of recession on our staff, required business levels cannot be maintained in the current economic climate.
“The proposed redundancies are spread geographically across our locations in Witney, Oxfordshire, Aberdeen and Glasgow.
“The employees affected come from a combination of departments. Enhanced redundancy packages and a full Employee Assistance Programme is being provided to those affected.”
He said no other division within the Stewart Milne Group was affected.