Indoor navigation systems for common users have recently received a lot of interest. Since the penetration of indoor navigation applications and location-based services strongly relies on accurate indoor maps such as blueprints. Navigation or positioning systems have been widely developed for Location-Based Services (LBS) applications and it comes along with a keen demand of indoor floor plans for displaying results even improving the positioning performance. Generally, the floor plans produced by sketch maps are not accurate enough to incorporate to the indoor positioning system. This study concentrates on generating the highly accurate floor plans based on the robot mapping technique using the portable mapping system. To improve the accuracy of floor plans and transform them into the global coordinate system for seamless applications, this study builds a testing and calibration field using the traditional outdoor control survey method implemented in indoor environments for evaluating the absolute accuracy of floor plans and map rectification. Based on an indoor control survey, this study proposes a novel procedure for building indoor floor plans that includes data acquisition and a map rectification method using the affine transformation to solve the scale and deformation problems in traditional sketch maps. This study presents the map rectification method and transfers the map coordinate from local coordinate system into world coordinate system such as WGS84. The preliminary results presented in this study illustrate that the final version of the building floor plan reach 1-meter absolute positioning accuracy using the proposed portable mapping systems and rectified sketch maps that combine with the map rectification. These maps are also applied in smart-phone based indoor navigation system and achieve the 1to 2-meter positioning accuracy.