With the continued scaling down of CMOS devices beyond 50 nm, accurate and precise measurements of gate dielectric layer thickness and dopant profiles in ultra shallow junctions are no more simple and straightforward even with sophisticated techniques. In this presentation, the current status and remaining issues in analytical methodology for gate oxides and ultra shallow junctions are summarized and discussed. For accurate measurement of nm gate oxides thickness with sub atomic layer thickness precision, the thickness that each technique generates can be different and the difference should be understood in a complementary nature. Compared and discussed are the differences between high resolution transmission electron microscopy, grazing incidence X-ray reflectivity, medium energy ion scattering spectrometry, X-ray photoelectron spectroscopy, ellipsometry for accurate and precise determination of gate oxides down to sub nm thickness. For ultra shallow junction depth profiling, details of the sputtering processes in low energy secondary ion mass spectrometry are investigated regarding to the damage profiles and surface transient sputtering effect. Development of multiple delta layer reference thin films for ultra shallow junction profiling is reported on the growth and the application for sputtering rate calibration including the surface transient effect. Relevant activities of ISO TC 201 Surface Chemical Analysis and CCQM Surface and Micro/Nano Analysis WG and the present status and issues of reference thin films for gate oxide thickness determination and ultra shallow junction profiling will be briefly discussed.