Today, nanoclays are important due to the wide applications in the industry and their unique features such as platelet structure, low cost, availability, possibility of surface spacing and surface chemistry changes, high ion exchange capacity. Nanoclay is purfied clay from other minerals which specified particle size distribution (usually less than 2 microns) and at least one of its dimensions would be in the nanometer range. Hence, in this study, a novel two-step method was tested for producing purified nanoclay from three different Bentonite region. The purification processes effect of on the final characteristics of clay and its impact on modified cation with organic molecules was investigated.This new method involves combining of physical and chemical methods for the purification of nanoclay. In these samples there were two main impurities, cristobalite and calcite, that were dissolved using a chemical dissolution method by using NaOH and HCL in order to get the highest purified montmorillonite with least changes in its. In the second step other impurities were separated using a physical sedimentation by using centrifugal force. The results showed that separation of all of the impurities by only physical methods is almost impossible and require using the chemical dissolution of impurities for removing them all is necessary. Further analysis showed that concentration and chemical reaction time are important to dissolve the impurities and excessive increase of these parameters effect montmorillonite structure. After these steps to change the distance between the clay plates the hexa decyl trimethyl ammonium Bromide ( HDTMA-Br)was used. The results showed that the modification step is directly affected by the purification step. This means that in case of the physical purification alone (which is incapable of separating all impurities) the after modification behavior of nonoclay is like raw bentonite. After purification by both physical and chemical methods, arrangement of HDTMA-Br in montmorillonite plates is regular and modified nanoclay has a regular pattern in the distance between the plate and the structure. The results face the presented previous report with this challenge that nanoclay purification only with physical separation may have challenges in many cases. To overcome these challenges using chemical dissolution techniques in addition to physical separation is recommended.