The method of identifying first order plus time delay transfer function model proposed for unstable systems by Ananth and Chidambaram [Closed loop identification to transfer function model for unstable systems, J. Franklin Inst. 336 (1999) 1055-1061] is modified to avoid the stability problems [Cheres, Parameter estimation of an unstable system with a PID controller in a closed loop configuration, J. Franklin Inst., 2005, accepted for publication] of the method. Two modifications are proposed. In the first modification of the method, the under-determined algebraic equations problem is converted into an optimization problem for calculation of the three parameters of the first order plus time delay (FOPTD) model. A simple method is given for the initial guess values of the model parameters. In the second approach, from the definition of Laplace transform of the output response, a third equation is formulated. The resulted three equations, in terms of the three parameters of the transfer function model, are then numerically solved. Simulation results are given for the second order plus time delay transfer function considered by Cheres 2005 [Parameter estimation of an unstable system with a PID controller in a closed loop configuration, J. Franklin Inst., 2005, accepted for publication]. The responses of the identified models with the same PID controllers are compared with that of the actual system. PID controllers are designed based on the identified models. The closed loop responses of the controllers on the original system are evaluated and compared. The present methods give better control performances. © 2005 The Franklin Institute. Published by Elsevier Ltd. All rights reserved.