In December 1864 and January 1865, Major Clemens served as chief signal officer to Admiral David D. Porter in the two attacks on Fort Fisher. He was also one of the soldiers who escorted President Lincoln when he visited Richmond in April 1865, shortly after the Confederate capital was evacuated.
During the attacks on Fort Fisher, he was aboard the admiral's flagship, the USS Malvern. It was his job to coordinate signals between the Army force ashore and the naval units.
Around midnight, January 16, 1865. he wrote his father: "I am in the midst of excitement and am so completely worn out and tired that it would be impossible for me to write much. We have been fighting all day (January 15) and fighting hard and I have been kept busy from daylight until now and even now I may be called at any moment to receive messages."