Raynolds returned to Washington at the outbreak of the war, and was made chief topographic engineer of the Department of Virginia in July 1861. The army lacked adequate maps for military use, so Raynolds and his team of engineers began to survey and draw up maps of Virginia and the region of the western portion of that state that had remained loyal to the Union and would become the new state of West Virginia. In 1862, Raynolds was engaged with John C. Frémont's Mountain Department in chasing Stonewall Jackson up the Shenandoah Valley and participated in the Battle of Cross Keys.