Mahima,
The latest version of Flex (v.11) allows the following parameters to be estimated by PEST within Flex: conductivity, storage, UZF static and transient parameters, recharge and evapotranspiration. If you would like to use PEST to estimate other parameters, please use PEST outside of the Flex environment to build your PEST interface (i.e., control file and other related inputs to PEST). This of course requires more in depth knowledge of PEST and the way Flex builds the PEST interface for your model. As a matter of fact, you may manually modify the PEST interface built by Flex for the supported parameters by adding the new parameters and parameter groups to the control file along with related changes to some of the control variables, and build the necessary PEST template file(s). If you do that, you can then run PEST within the Flex interface.
András