Pyramid shaped pyrolysis flame is a new method for carbon nanotubes (CNTs) synthesis, using this method has successfully produced high properties carbon nanotubes. But, because at the first 1min of sampling time, there are not tubes produced, so catalyst particles and carbon atom clusters assemble on the sampling substrate in the first 1min. Also, lots of amorphous carbon, deformity tubes, and graphite segment were produced in the experimental. In order to eliminate these impurities, ultrasonic treatment, aether cleaning, acid pickling, and co-processing were used. Ultrasonic treatment can separate particles from tubes, aether can clear amorphous carbon and graphite segment while acid pickling can dissolve catalyst particles. Using ultrasonic oscillation separation and aether as diluent can gain pure sample. Ultrasonic oscillation and nitric acid as diluent can purify products also, but not as good as aether as diluent. Concentrated nitric acid and long time immersion will destroy the structure of carbon nanotubes.