We demonstrate scanning tunneling microscopy studies of a Si(001)-c(4x4) structure which consists of a considerable number of dimer vacancies (missing dimers). Two different preparation methods are examined; one is hydrogen desorption and another is a special annealing and cooling process without hydrogen. The STM images reveal that atomic structure of the c(4x4) prepared without hydrogen is quite different from that prepared with hydrogen and is well described by the missing dimer model. A moire-like pattern is observed on the c(4x4) surface prepared by hydrogen with an increase in the tip-sample distance, which suggests that the atoms lying in the subsurface should be considered for the precise description of the c(4x4) structure.