In 1888, Miller was transferred to the Caledonian Railway's drawing office in Glasgow, and designed a number of railway stations in the West of Scotland under the supervision of the engineer-in-chief, George Graham, and Donald Alexander Matheson, who was to become his successor. Notable designs from this period include the English-domestic style stations at Fort Matilda (1889), Troon (1892) and West Kilbride (1900), and the interchanges between rail and steamer at Gourock Pier (1889) and Greenock Princes Pier (1893). In 1892, having won the competition to design Belmont Church in Hillhead, he set up in full-time practice on his own account and rented an office at 223 West George Street, Glasgow. He continued to design for the Caledonian and other Scottish railway companies, including the distinctive 'chalet style' stations on the West Highland Railway in 1894, and the Scottish Jacobean-style St Enoch subway station for the Glasgow District Subway Company.