Magnetic Weyl semimetals exhibit intriguing transport phenomena due to their non-trivial band structure. Recent experiments in bulk crystals of the shandite-type Co$_3$Sn$_2$S$_2$ have shown that this material system is a magnetic Weyl semimetal. To access the length scales relevant for chiral transport, it is mandatory to fabricate microstructures of this fascinating compound. We therefore have cut micro-ribbons (typical size $0.3~times~3~times~50$mu$m^3$) from Co$_3$Sn$_2$S$_2$ single crystals using a focused beam of Ga$^{2+}$-ions and investigated the impact of the sample dimensions and possible surface doping on the magnetotransport properties. The large intrinsic anomalous Hall effect observed in the micro ribbons is quantitatively consistent with the one in bulk samples. Our results show that focused ion beam cutting can be used for nano-patterning single crystalline Co$_3$Sn$_2$S$_2$, enabling future transport experiments in complex microstructures of this Weyl semimetal.