Prehistoric archaeological sites consist significant part of the discovered archaeological objects in Israel. Among different geophysical methods applied at the Prehistoric sites in Israel, detailed magnetic investigations play the most important role. The rapid and reliable investigations allow consistently estimate the possible archaeological significance of the area under study. Interpretation of magnetic surveys in Israel is complicated by several factors, the most significant from which is a strong oblique magnetization of the Earth's magnetic field (about 45°). The variable structure of the upper part of the geological section often does not allow to determine the level of the normal magnetic field within the studied sites. Noise caused by iron objects and electric power lines sometimes reaches high values. Uneven topography also disturbs the effect from the archaeological targets. The complicated conditions of the survey require advanced methods for delineation of buried objects, their quantitative interpretation and 3-D modeling. We present here results of detailed magnetic investigations at four most typical objects: Eynan site of Natufian period (northern Israel), Nahal Zehora site of Pottery Neolithic period (northern Israel), Kissufim Road of Chalcolitic period (southern Israel) and multilevel Proto-Historic site Tel Megiddo (northern Israel).