If you upgrade to R2018a, this process is a little more straightforward, but this code will work in R2016a.
Step 1: Import your data and update the variable names:
t = readtable('Test.csv','ReadVariableNames',true);
t.Properties.VariableNames{1} = 'Time';
Step 2: Convert the first column to duration. I cheat a little and use datetime to do the conversions. Note that this step is done automatically in R2018a, so you can skip it. In addition, in R2018a, you can do the conversion by calling duration directly, instead of using datetime.
t.Time= datetime(t.Time,'InputFormat','HH:mm:ss.SSS')-datetime('today');
t.Time.Format = 'hh:mm:ss.SSS';
Step 3: Plot
plot(t.Time, [t.Sample1 t.Sample2],'.-');
