This work reports the system integration of the underwater seafloor laser scanner, designed and fabricated by Institute of Undersea Technology, National Sun Yat-sen University, with the in situ porosity measurement system, known as IMP2, developed by Applied Physics Lab, University of Washington. Our original prototype underwater seafloor laser scanner worked more like an indoor experimental setup rather than an instrument. It is the goal of this work to modify the detail design of hardware and software of the system such that the operation of the scanner and the data analysis of the results can be done like a commercial instrument. Our laser scanning module adopts structural light method with a single camera approach. The calibration of the camera is achieved with a template board on which sets of grid points are laid with numerical control milling machine. These grid points are used to create longitudinal and latitudinal lines for pixel-to-coordinate conversion. Three sub-pixel sampling methods, namely, intensity weighted centroid, second order polynomial intensity fitting and Gaussian intensity fitting, are developed to locate the center of the laser light strip on pixel plane and to be converted into engineering coordinates. For the convenience of post-processing, grid point meshing and spectrum analysis packages are built-in to provide standard output for further studies. The overall performance of the system was validated by four tests in indoor tanks and field as well. One scanning in air was undertaken to verify if synchronization signal between the laser scanner and the motion of the linear track was correct; several models of known dimension were placed in the water tank for scanning to see if the system reaches the desired accuracy; an integration of the laser scanner and the IMP2 was tested prior to the deployment in the sea, and a scanning a artificial seafloor model of known spatial spectra indicated the proper functioning of the combined system; finally a successful 20-meter deep field deployment and retrieve assured the bases for the acquisition of seafloor roughness field for acoustics related research.