We propose a modification to the standard Bayer color filter array (CFA) and photodiode structure for CMOS image sensors, which we call 2PFCTM (two pixels, full color). The blue and red filters of the Bayer pattern are replaced by a magenta filter. Under each magenta filter are two stacked, pinned photodiodes; the diode nearest the surface absorbs mostly blue light, and the deeper diode absorbs mostly red light. The magenta filter absorbs green light, improving color separation between the blue and red diodes. We first present a frequency-based demosaicing method, which takes advantage of the new 2PFC geometry. Due to the spatial arrangement of red, green, and blue pixels, luminance and chrominance are very well separated in the Fourier space, allowing for computationally inexpensive linear filtering. In comparison with state-of-the-art demosaicing methods for the Bayer CFA, we show that our sensor and demosaicing method outperform the others in terms of color aliasing, peak signal to noise ratio, and zipper effect. As demosaicing alone does not determine image quality, we also analyze the whole system performance in terms of resolution and noise.