#99 was primarily used for paying postage on high-value letters, specifically international mail and heavy domestic letters during the late 1860s. Its main purposes included:

Mail to England: In 1866, the postal rate for a letter from the United States to England was 24 cents per half-ounce. This rate applied to letters carried by either United States or British packet ships (such as Cunard). Out of the 24 cents, a portion was designated for the transatlantic packet (often 16 cents) and the rest for inland postage (4 cents in each country). The 24¢ rate was replaced with the lower treaty rate in January 1st, 1868 of 12¢ per half-ounce.
Other usage: It was used for heavier of high value letters domestically. It as also used as make up postage for foriegn destinations, an example is shown above.