The term “clean CR” refers to a continuing resolution bill, a type of appropriations legislation passed by Congress, without attached conditions. Continuing resolutions generally maintain the level of government funding of the previous fiscal year, and are used when appropriations bills were not passed due to an impasse in budget negotiations.
If the House and Senate cannot agree on regular appropriations bills, the continuing resolution can be used. A continuing resolution takes the form of a joint resolution by the House and the Senate and bridges funding for existing federal programs.
Insisting on conditions to the continuing resolution may continue the same impasse that forced the budget negotiations to break down in the first place. For example, in 2013, the House of Representatives and Senate failed to pass appropriations bills shortly before the start of the fiscal year. The House of Representatives insisted that appropriations bills also defund the Affordable Care Act. When the Senate did not agree to it, and a continuing resolution was proposed to prevent a government shutdown, the House insisted that the continuing resolution be conditioned on delaying the implementation of the Affordable Care Act. Had the Congress agreed on a clean CR, the government shutdown could have been avoided.