Chakra sometimes appears physically, as opposed to just being used as the power source for jutsus. Some examples of this are when the Hyuugas are using the Gentle Fist technique or when Naruto is using the Kyuubi chakra. In the first example, the chakra is sometimes used to block things, such as in Neji's Rotation jutsu, while Naruto's chakra has the appearance of fire and has at least once actually burned Sakura. Is there any set rule to how chakra acts physically or what it can or cannot do when not being used as the energy source for a specific jutsu?
Normaly ninja's should only be able to use their chakra to cast jutsu, there is practicly no limit to what they can do with this
Normal chakra is a form of energy all living individuals naturally produce to some degree. Contained in the "chakra coils" that mainly surround and connect to each chakra-producing organ, the energy circulates throughout the body in a network called the "chakra circulatory system" (similar to the cardiovascular system)
It seems only highly trained people can use chakra so that it is visible .
Certain groups, such as ninja, have learned to generate more chakra and release it outside their bodies through their "chakra points" (tenketsu) in order to perform special techniques (jutsu). Chakra is not normally visible to the human eye, though chakra can be seen in situations where a person releases as much of their chakra as possible. This is rarely seen due to the restrictions of certain chakra points (Eight Gates), limiting the amount of chakra an individual can release at a single given time. Chakra can also be visible when doing specific techniques (such as the Rasengan) which take a high degree of chakra control to perform.
For a pretty detaild explaination about chakra you can check the naruto wiki right here