The achievement description indicates you need 101 or more underground malls, but it unlocks when you reach 100. A subway mall is a passive structure, in that you cannot build it directly. Instead, your population builds them when the circumstances are correct. You need to have a large population, multiple tube stations (underground railway, essentially) and underground materials yards. Because of the population requirement, I recommend working on this simultaneously with Bustling Metropolis. It can be completed on any map.
This is likely the single longest achievement in the game, but can be completed while sleeping or other AFK activities. Start by building a resource center and reach around $5 billion. Build a second resource center, but instead of convenience stores build Flat 5 (under Construction, Housing) until you have 80-100k population. You can view your current population under the Report menu. It is the fourth line from the top on the City Info report, and is labeled as "Pop. Change/Year." The label really refers to the graph below as the number on this line is your current population.
You are going to build tube stations underneath your housing resource center, so start by pressing twice to select the Cutaway menu, use to select the second level from the bottom, and press and then . The screen should largely be orange at this point, indicating you are underground. Proceed to build a two-line underground railroad that starts at the edge of the map and goes lengthwise underneath your housing resource center. Along the way, build 6 2-line tube stations, each one 3-5 rail away from the next. Try to keep all the stations close to the housing above, which means you may need to build the line in a U-shape.
When placing the tube stations, note they have a platform for people to walk on. This is the side that the subway malls will be built from. Place two Material Yards on the other side of each station, leaving the platform side free for the Subway Malls to be built. If you make a U-shape, make sure these sides are facing the outside of the U to avoid potential interference with each other.
Build two trains: a DC-4 with layout 2, and a Tube train (all the way on the bottom of the list when purchasing trains). For each station in the line, you need to set the DC-4 to Unload only. For the Tube train, you can delete the rail leading off the map to speed things up a little, so that it only shuttles between the stations.
At this point, you just have to wait. I set it to run overnight, and it took about 12 hours total over two nights for 100 stores to build. If you are following the road map, now is a good time to work on Top Trader achievement.