By rapid thermal annealing the Ni film evaporated on thin SiO2 layer covered Si substrate, we have successfully demonstrated the self-aggregation of two-dimensional randomized Ni nano-dots on Si wafer. The thin oxide layer prevents the formation of NiSi2 compounds and facilitates the self-assembly of Ni nanodots from retaining the thermal power on SiO2 layer. This greatly shrinks the annealing time required for metallic nanodot formation from >10 min to <30 sec. With the advantage of the self-assemble Ni/SiO2 nano-dots based nano-mask, a large-area Si nano-pillar array with rod size of <50 nm can be formatted on Si substrate through the induced coupled plasma reactive ion etching (ICP-RIE) procedure. After removing Ni dots and the SiO2 film on the Si substrate, both the visible and near infrared photoluminescence from the Si nano-pillar sample were observed and analyzed.