Layered van der Waals transition metal dichalcogenides (TMDCs), generally composed of three atomic X-M-X planes in each layer (M = transition metal, X = chalcogen), provide versatile platforms for exploring diverse quantum phenomena. In each MX2 layer, the M-X bonds are predominantly covalent in nature, as a result, the cleavage of TMDC crystals always occurring between the layers. Here we report the controllable realization of fractional-layer WTe2 via an in-situ scanning tunnelling microscopy (STM) tip manipulation technique. By applying STM tip pulses, hundreds of the topmost Te atoms are removed to form a nanoscale monolayer Te pit in the 1T'-WTe2, thus realizing a brand-new 2/3-layer WTe2. Such a unique configuration undergoes a spontaneous atomic reconstruction, yielding an energy-dependent unidirectional charge-density-wave state with the wavevector and geometry quite distinct from that of pristine 1T'-WTe2. Our results expand the conventional understanding of the TMDCs and are expected to stimulate the research on extraordinary structures and properties based on fractional-layer TMDCs.