What plant are you working with?  Arabidopsis?  Different plants have different root anatomies and split root systems can be induced by different methods.  Tomato and bean plants easily produce adventitious roots, for instance, and these can be trained into different pots.  You could grow a normal plant, cut off the top and place it in water to develop clean adventitious roots.  I've never worked with arabidopsis.

basically! Pepper and eagplant for now ...beans also ... is it same to tomatoes' roots? 

is there anything to be carfull about when transplanting!?

I care about infestation "I should take off if any infestation happens before the traitement ... to secure off biases ... 

first tries to be done before the test but I still need to check 

thank you NIna 

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It depends on type of root

Everything in the Solanaceae is easy to root.  Obviously when transplanting it is essential not to break roots- the problem might be that you get so many adventitious roots you have to pull some off to get the two you want for a two pot system.  You can often get the plant to produce roots at the site you want by scraping the epidermis: roots will form at the wound site.  I don't know what your goal is:  when I work with roots, I often plant in "Turface MVP" a highly fired monmorillonite clay substrate with a high CEC and good drainage that easily cleans off roots. If I want to analyze the roots after the experiment, I really appreciate having them clean.