Istanbul hosts large amount of historical buildings. Many of these buildings are made of limestone, fossiliferous limestone and clayey limestone widely known in the region as "Kufeki Stones". In this study the effect of varying cleaning techniques on altered Kufeki stones was investigated. Within this respect, fresh Kufeki stone samples from original building stone (Bakirkoy Kufekisi) and recently used substitute rocks from different quarries and regions around Istanbul were compiled. Mineralogical, petrographic and chemical analysis followed by physical and mechanical properties were investigated for these stones. Same stone samples were subjected to accelerated deterioration mechanisms. These altered stones were then cleaned with laser cleaning and pressurized micro-sand blasting techniques and weight losses were calculated and visual changes were determined. The results revealed that rock micro-texture and physical properties should be considered in determining the appropriate cleaning technique. Besides, the usage type of the stone and type of deterioration mechanism should also be considered during the determination of cleaning technique. It is also emphasized that the laser cleaning is less destructive method for cleaning Kufeki stones among the investigated techniques.