ASCE 4 requires that a hard stop be built around the seismic isolation system in nuclear power plants. In order to maintain the function of the isolation system, this hard stop is required to have clearance-to-stop, which should be no less than the 90th-percentile displacements for 150% Design Basis Earthquake (DBE) shaking. Huang et al. calculated clearance-to-stop by using a Latin Hypercube Sampling technique, without considering the rocking behavior of the isolated structure. This paper investigates the effects on estimation of clearance-to-stop due to 1) rocking behavior of the isolated structure and 2) sampling technique for considering the uncertainties of isolation system. This paper explains the simplified analysis model to consider the rocking behavior of the isolated structure, and the input earthquakes recorded at Diablo Canyon in the western United States. In order to more accurately approximate the distribution tail of the horizontal displacement in the isolated structure, a modified Latin Hypercube Sampling technique is proposed, and then this technique was applied to consider the uncertainty of the isolation system. Through the use of this technique, it was found that rocking behavior has no significant effect on horizontal displacement (and thus clearance-to-stop) of the isolated structure, and the modified Latin Hypercube Sampling technique more accurately approximates the distribution tail of the horizontal displacement than the existing Latin Hypercube Sampling technique.