Microscopic topological and spectroscopic properties of the ultrathin silicon interface control layer (Si-ICL) grown by molecular beam epitaxy on the (001) GaAs surface were investigated by the ultrahigh vacuum (UHV), scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS) techniques, and the results were correlated with the macroscopic electronic properties measured by in situ X-ray photoelectron spectroscopy (XPS) and UHV photoluminescence (PL) techniques. Growth of the Si-ICL on c(4 x 4) GaAs surface produced much more ordered STM topology, leading to better electronic properties as observed by XPS, PL and STS methods than the growth on (2 x 4) surface. In addition to normal STS spectra showing GaAs energy gap, many anomalous spectra showing much wider apparent gaps were observed on all the surfaces, and they were interpreted to correspond to the pinning centers for the Fermi level where surface states exchange electronic charge with the STM tip and modify the band bending.