You can register filters when you are setting up your MockMvc
using MockMvcBuilders
.
MockMvc mockMvc = MockMvcBuilders
.webAppContextSetup(webApplicationContext)
.addFilter(filter, urlPatterns);
The javadoc has more details. This method of registering filters is (mock-)equivalent to the web.xml configuration. For example
<filter-mapping>
<filter-name>filter</filter-name>
<url-pattern>/*</url-pattern>
</filter-mapping>