In this paper, a finite memory structure (FMS) filtering with two kinds of measurement windows is proposed using the chi-square test statistic to cover nominal systems as well as temporarily uncertain systems. First, the simple matrix form for the FMS filter is developed from the conditional density of the current state given finite past measurements. Then, one of the two FMS filters, the primary FMS filter or the secondary FMS filter, with different measurement windows is operated selectively according to the presence or absence of uncertainty, to obtain a valid estimate. The primary FMS filter is selected for the nominal system and the secondary FMS filter is selected for the temporarily uncertain system, respectively. A declaration rule is defined to indicate the presence or absence of uncertainty, operate the suitable one from two filters, and then obtain the valid filtered estimate. A test variable for the declaration rule is developed using a chi-square test statistic from the estimation error and compared to a precomputed threshold. In order to verify the proposed selective FMS filtering and compare with the existing FMS filter and the infinite memory structure (IMS) filter, computer simulations are performed for a selection of dynamic systems including a F404 gas turbine aircraft engine and an electric motor. Simulation results confirm that the proposed selective FMS filtering works well for nominal systems as well as temporarily uncertain systems. In addition, the proposed selective FMS filtering is shown to be remarkably better than the IMS filtering for the temporarily uncertain system.