We have designed, simulated, and fabricated micro-magnetic substrates for the reversible self-assembly of cell-internalized magnetic fluorescent nanoparticles according to lithographically defined patterns within live cells. Magnetic nanoparticles have recently demonstrated potential in activating highly specific activity within single cells. Using microfabrication, we have developed a technique of localizing both particles and large magnetic fields to highly specific, engineered, sub-cellular locations with various modes of operation. The substrates were simulated in 3 dimensions with ANSYS FEA, and consist of micro-patterned, electroplated permalloy elements planarized with SU-8. Various modes of magnet-orientation dependent patterns of nanoparticles were generated and verified within live cells, with their precise location verified under separate blue and green (absorption and emission wavelengths of the particles) filters using a fluorescent microscope. Results correspond well with modeled positions and response time. We anticipate using the tool as a compact, simple method of generating highly localized, easily distinguishable, sub-cellular chemical and mechanical signals that is compatible with standard biological fluorescence setups.