For anyone in the same situation, here is the solution:
opt = ssestOptions;
opt.EnforceStability = 1;
A = 0; % initial value
B = [0 0];
C = 1;
D = [0 0];
Ts = 0; % Continuous time
init_sys = idss(A,B,C,D,'Ts',Ts);
% Set C and D structures as fixed (use values from intialized state space
% system init_sys
init_sys.Structure.A.Free = true;
init_sys.Structure.B.Free = true;
init_sys.Structure.C.Free = false;
init_sys.Structure.D.Free = false;
init_sys.Structure.K.Free = true;
% estimate model based on the data
constrained_stateSpace_model = ssest(your data,init_sys,opt);