We report a periodic two-dimensional (2D) array of uniquely shaped dotlike nanoprotrusions (NPs), which simultaneously self-organize on a Si surface under pulsed laser irradiation. The shape of the dotlike NPs can be controlled by adjusting the number of laser pulses. The flask-shaped dotlike NP array is named a vidro-nanodot (VND) array. We present a detailed analysis of the internal structure of VND using high-resolution electron microscopy. (C) 2011 The Japan Society of Applied Physics