Results of atomic force microscope (AFM) and scanning tunneling microscope (STM) studies of superlattices and long-range modulations induced by impurities in transition metal chalcogenides are presented. Superlattices formed by Fe intercalation into the van der Waals gaps of 2H-NbSe2, 2H-TaSe2 and 2H-TaS2 show ordered occupation of the octahedral holes and STM spectroscopy shows density-wave energy gaps existing in the antiferromagnetic phases. In NbSe3, interstitial impurities such as Fe, Co, Cr, and V induce long-range modulated structures that can be detected at room temperature with AFM scans. These modulations modify the charge-density wave structure forming at low temperature and STM spectroscopy has been used to measure these changes.