The first successful development of a roll to roll (R2R) process that applies an external magnetic field to orient and organize magnetic nanoparticles along nanocolumns in the thickness direction of thin films to obtain high electrical and thermal conductivities in the thickness direction is reported. Utilizing a R2Rmachine that includes an in-line electromagnet, we orient and organize Ni nanoparticles in nanocolumns inside a flexible poly(dimethylsiloxane) matrix. In these films, the nanocolumns of Niparticles point in the magnetic field/thickness direction which leads to enhancement of the electrical and thermal conductivity in the thickness direction while maintaining optical transparency as the space between the nanocolumns is depleted of nanoparticles facilitating unimpeded light transmission. Exhibiting piezoresistivity, the electrical conductivity in these films increases by as much as 7 orders under moderate pressures. The thermal conductivity of the aligned composite films filled with 14 vol % Ni flakes was found to increase to 50 times the conductivity of the polymer matrix, or 13 times the conductivity of the non-aligned composite with the same concentration. This R2R method facilitates the manufacture of unique films with enhanced functional properties in the thickness direction to be used in a range of applications including Z direction heat spreaders, transparent switches, privacy protection screens and piezoresistive sensors.