Subramaniam was born in Madras to V. Lakshminarayana Iyer and Seethalakshmi, both accomplished musicians. He lived in Jaffna during his younger years, taking up music studies before the age of five. He began training in violin under the tutelage of his father, Professor V. Lakshminarayana. "Mani", as he is fondly known by fellow musicians and his family, gave his first public performance at the age of six. His uncles include Ramnad Raghavan and Ramnad Krishnan. His brothers are also acclaimed musicians, and include the violinist-composers L. Shankar, and the late L. Vaidyanathan. He has released recordings with both. Subramaniam developed a passion for music as well as science from a young age, studying Medicine and acquiring his M.B.B.S. at Madras Medical College. He registered as a General Practitioner, before deciding to pursue music full-time. He has a master's degree in Western classical music, which he acquired at the California Institute of the Arts.