It is not recommended to use individual variables for that purpose.
http://matlab.wikia.com/wiki/FAQ#How_can_I_process_a_sequence_of_files.3F http://matlab.wikia.com/wiki/FAQ#How_can_I_create_variables_A1.2C_A2.2C....2CA10_in_a_loop.3F
After you load the data from any one file, you can use size() to check the number of columns, and add it to a cell array of data if it is one of the ones you want to keep. After you have loaded them all you can use the cell array to produce an appropriate plot.