The interaction between gold nanoparticles and femtosecond laser irradiation has been shown to be effective in damaging malignant cells in two-dimensional cell cultures. Studies with rodent models have shown promising results. However, rodent physiology and genetics are known to differ substantially from that of humans. For bridging the gap between two-dimensional cell cultures and animal models for plasmonic phototherapy, we use a natural hydrogel as a three dimensional scaffold for growing breast cancer epithelial cells in co-culture with healthy fibroblast cells. The malignant cells were specifically targeted using anti-EGFR-coated gold nanospheres, and irradiated by amplified femtosecond pulses at off-resonance wavelength of 800 nm. Irradiated cell colonies seized to develop and grow; after approximately three days, widespread death of both normal fibroblasts and malignant epithelial cells, lead to disintegration of all cell colonies. Overall, we have found that cells in three-dimensional cultures are considerably more resistant to the effect of the irradiation.